Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1354
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: 49113
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1880 original size:13 final size:13
Alignment explanation
Indices: 1850--1881 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1840 CCCCTTAAAC
1850 CCACCAA-ACCCT
1 CCACCAACACCCT
1862 -CACCAACACCCT
1 CCACCAACACCCT
1874 CCACCAAC
1 CCACCAAC
1882 CCACACCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 5 0.28
13 7 0.39
ACGTcount: A:0.34, C:0.59, G:0.00, T:0.06
Consensus pattern (13 bp):
CCACCAACACCCT
Found at i:1986 original size:1 final size:1
Alignment explanation
Indices: 1980--2061 Score: 137
Period size: 1 Copynumber: 82.0 Consensus size: 1
1970 ACCAAACAAC
* * *
1980 TTTTTTTTTTTTCTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2045 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
2062 GTTTGGGGCT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (1 bp):
T
Found at i:2117 original size:23 final size:23
Alignment explanation
Indices: 2091--2136 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2081 GTTGTTGGGG
*
2091 GTTGTGTTTGGGTGTTGT-GTTTT
1 GTTGTGTCTGGG-GTTGTGGTTTT
2114 GTTGTGTCTGGGGTTGTGGTTTT
1 GTTGTGTCTGGGGTTGTGGTTTT
2137 TTTGGTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.00, C:0.02, G:0.41, T:0.57
Consensus pattern (23 bp):
GTTGTGTCTGGGGTTGTGGTTTT
Found at i:2207 original size:41 final size:40
Alignment explanation
Indices: 2125--2217 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 40
2115 TTGTGTCTGG
* *
2125 GGTTGTGGTTTTTTTGGTTGGTGTGTGTTGGGTTGGGGGGT
1 GGTTG-GGTTTTTTTGGTTGGTGGGTGTGGGGTTGGGGGGT
* *
2166 GGTTGGGTTTTTTGTGGTTTGTGGGTG-GGGGTTGGTTGGGT
1 GGTTGGGTTTTTT-TGGTTGGTGGGTGTGGGGTTGG-GGGGT
2207 GTGTT-GGTTTT
1 G-GTTGGGTTTT
2218 GGCGTTGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
40 15 0.33
41 27 0.60
42 3 0.07
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (40 bp):
GGTTGGGTTTTTTTGGTTGGTGGGTGTGGGGTTGGGGGGT
Found at i:2404 original size:19 final size:21
Alignment explanation
Indices: 2322--2411 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 21
2312 TGGTTGGGTT
*
2322 TTGTGTTGTGTGGG-GG-GGTG
1 TTGTGTTGGGTGGGTGGTGG-G
*
2342 CTTGT-TTGGGCTGGTGTGGTCGG
1 -TTGTGTTGGG-TGG-GTGGTGGG
*
2365 TTGTTTTGGGTGGGTTGGTGGG
1 TTGTGTTGGGTGGG-TGGTGGG
2387 TTGTGTT-GG-GGGTGGTGGG
1 TTGTGTTGGGTGGGTGGTGGG
2406 TT-TGTT
1 TTGTGTT
2412 TTGTGGTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
18 4 0.07
19 9 0.15
20 7 0.12
21 10 0.17
22 20 0.34
23 8 0.14
24 1 0.02
ACGTcount: A:0.00, C:0.03, G:0.53, T:0.43
Consensus pattern (21 bp):
TTGTGTTGGGTGGGTGGTGGG
Found at i:2676 original size:39 final size:37
Alignment explanation
Indices: 2611--2689 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 37
2601 CAACACAACA
2611 CCCAACCCAAAACAAAAACAACCAAACCCAAACAACCACC
1 CCCAACCCAAAACAAAAACAACCAAA--CAAA-AACCACC
2651 CCCAA-CCAAAACCCAAAAAC-A-CAAACAAAAACCACC
1 CCCAACCCAAAA--CAAAAACAACCAAACAAAAACCACC
2687 CCC
1 CCC
2690 CCCTCCCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
36 10 0.27
37 4 0.11
39 10 0.27
40 6 0.16
41 7 0.19
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (37 bp):
CCCAACCCAAAACAAAAACAACCAAACAAAAACCACC
Found at i:2824 original size:17 final size:16
Alignment explanation
Indices: 2797--2868 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 16
2787 GTGTGGGGTT
*
2797 GGGGTGGGGGGTGTGG
1 GGGGTGTGGGGTGTGG
2813 GTGGGTGTGGGG-G-GG
1 G-GGGTGTGGGGTGTGG
2828 GGTTGGTGTGGGGTGTGG
1 GG--GGTGTGGGGTGTGG
* *
2846 GGGGGGTTGGGGTTTGG
1 GGGGTG-TGGGGTGTGG
2863 GGGGTG
1 GGGGTG
2869 GTGTGGGGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.02
15 3 0.07
16 14 0.30
17 24 0.52
18 4 0.09
ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25
Consensus pattern (16 bp):
GGGGTGTGGGGTGTGG
Found at i:2827 original size:22 final size:20
Alignment explanation
Indices: 2802--2892 Score: 73
Period size: 22 Copynumber: 4.4 Consensus size: 20
2792 GGGTTGGGGT
2802 GGGGGGTGTGGGTGGGTGTGGG
1 GGGGGGT-TGGG-GGGTGTGGG
2824 GGGGGGTTGGTGTGGG-GTGTGG
1 GGGGGGTTGG-G-GGGTGTG-GG
*
2846 GGGGGGTT--GGGGTTTGGG
1 GGGGGGTTGGGGGGTGTGGG
*
2864 GGGTGGTGTGGGGGGT-TGGG
1 GGGGGGT-TGGGGGGTGTGGG
2884 GGGGTGGTT
1 GGGG-GGTT
2893 TTGTGCGTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
18 11 0.19
19 4 0.07
20 8 0.14
21 14 0.24
22 22 0.37
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (20 bp):
GGGGGGTTGGGGGGTGTGGG
Found at i:2828 original size:23 final size:24
Alignment explanation
Indices: 2783--2851 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
2773 CAATGTTGGT
2783 GGTT-GTGTGGGGT-TGGGGTGGGG
1 GGTTGGTGTGGGGTGTGGGG-GGGG
2806 GGTGTGG-GT-GGGTGT-GGGGGGG
1 GGT-TGGTGTGGGGTGTGGGGGGGG
2828 GGTTGGTGTGGGGTGTGGGGGGGG
1 GGTTGGTGTGGGGTGTGGGGGGGG
2852 TTGGGGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
21 3 0.08
22 9 0.22
23 16 0.40
24 11 0.28
25 1 0.03
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (24 bp):
GGTTGGTGTGGGGTGTGGGGGGGG
Found at i:2830 original size:35 final size:36
Alignment explanation
Indices: 2791--2889 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
2781 GTGGTTGTGT
* *
2791 GGGGTTGGGGTGGGGGGTGTGGGTGGGTGTGGGG-G
1 GGGGTTGGTGTGGGGGGTGTGGGGGGGTGTGGGGTG
*
2826 GGGGTTGGTGTGGGGTGTG-GGGGGGGT-TGGGGTTTG
1 GGGGTTGGTGTGGGGGGTGTGGGGGGGTGTGGGG--TG
*
2862 GGGGGTGGTGTGGGGGGT-TGGGGGGGTG
1 GGGGTTGGTGTGGGGGGTGTGGGGGGGTG
2890 GTTTTGTGCG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
33 5 0.09
34 7 0.13
35 17 0.31
36 25 0.46
ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25
Consensus pattern (36 bp):
GGGGTTGGTGTGGGGGGTGTGGGGGGGTGTGGGGTG
Found at i:2856 original size:10 final size:10
Alignment explanation
Indices: 2802--2887 Score: 54
Period size: 10 Copynumber: 8.5 Consensus size: 10
2792 GGGTTGGGGT
2802 GGGGGGTGTGG
1 GGGGGGT-TGG
* *
2813 GTGGGTGTGGG
1 G-GGGGGTTGG
2824 GGGGGGTTGG
1 GGGGGGTTGG
*
2834 TGTGGGGTGTGG
1 -GGGGGGT-TGG
2846 GGGGGGTT--
1 GGGGGGTTGG
*
2854 -GGGGTTTGG
1 GGGGGGTTGG
*
2863 GGGGTGG-TGT
1 GGGG-GGTTGG
2873 GGGGGGTTGG
1 GGGGGGTTGG
2883 GGGGG
1 GGGGG
2888 TGGTTTTGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 17
0.68 0.12 0.20
Matches are distributed among these distances:
7 6 0.11
9 2 0.04
10 24 0.42
11 17 0.30
12 8 0.14
ACGTcount: A:0.00, C:0.00, G:0.76, T:0.24
Consensus pattern (10 bp):
GGGGGGTTGG
Found at i:2942 original size:1 final size:1
Alignment explanation
Indices: 2901--2933 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
2891 TTTTGTGCGT
*
2901 GGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2934 TTGTGGGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:2955 original size:1 final size:1
Alignment explanation
Indices: 2951--2980 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2941 GGTCCCCCCC
2951 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2981 ACCCCCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3144 original size:21 final size:22
Alignment explanation
Indices: 3090--3144 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
3080 TTTTGTGGGT
3090 TGGGGGGT-TT-TGGTTGGGGC
1 TGGGGGGTGTTGTGGTTGGGGC
*
3110 TGGGCGGGTG--GTGGTTGGTG-
1 TGGG-GGGTGTTGTGGTTGGGGC
3130 TGGGGGGTGTTGTGG
1 TGGGGGGTGTTGTGG
3145 GTTGTGGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 16 0.55
ACGTcount: A:0.00, C:0.04, G:0.64, T:0.33
Consensus pattern (22 bp):
TGGGGGGTGTTGTGGTTGGGGC
Found at i:3165 original size:15 final size:14
Alignment explanation
Indices: 3141--3180 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3131 GGGGGGTGTT
3141 GTGGGTTGTGGTGCGG
1 GTGGG-TGTGGTG-GG
3157 GTGGGTGTGGTGGG
1 GTGGGTGTGGTGGG
*
3171 GGGGGTGTGG
1 GTGGGTGTGG
3181 GTGTGGGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 7 0.30
16 5 0.22
ACGTcount: A:0.00, C:0.03, G:0.70, T:0.28
Consensus pattern (14 bp):
GTGGGTGTGGTGGG
Found at i:3182 original size:20 final size:20
Alignment explanation
Indices: 3157--3215 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3147 TGTGGTGCGG
3157 GTGGGTGTGGTGGGGGGGGT
1 GTGGGTGTGGTGGGGGGGGT
3177 GTGGGTGTGG-GGGGGGGG-
1 GTGGGTGTGGTGGGGGGGGT
*
3195 G-GGGTCTTGCGTGGGGGGGGT
1 GTGGGT-GTG-GTGGGGGGGGT
3216 TTTGCTTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.12
18 3 0.09
19 9 0.26
20 18 0.53
ACGTcount: A:0.00, C:0.03, G:0.75, T:0.22
Consensus pattern (20 bp):
GTGGGTGTGGTGGGGGGGGT
Found at i:3182 original size:24 final size:24
Alignment explanation
Indices: 3126--3199 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
3116 GGTGGTGGTT
* * *
3126 GGTGTGGG-GGGTGTTGTGGGTTGT
1 GGTGTGGGTGGGTGTGGTGGG-GGG
*
3150 GGTGCGGGTGGGTGTGGTGGGGGG
1 GGTGTGGGTGGGTGTGGTGGGGGG
*
3174 GGTGTGGGTGTGG-G-GGGGGGGGG
1 GGTGTGGGTG-GGTGTGGTGGGGGG
3197 GGT
1 GGT
3200 CTTGCGTGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
23 11 0.26
24 18 0.43
25 13 0.31
ACGTcount: A:0.00, C:0.01, G:0.73, T:0.26
Consensus pattern (24 bp):
GGTGTGGGTGGGTGTGGTGGGGGG
Found at i:3305 original size:14 final size:14
Alignment explanation
Indices: 3286--3327 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
3276 CCACCCACCA
3286 ACAAAACCCCCCAC
1 ACAAAACCCCCCAC
3300 ACAAAAAACCCCCC-C
1 AC--AAAACCCCCCAC
*
3315 ACAAAAACCCCCA
1 ACAAAACCCCCCA
3328 ACCAGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
13 9 0.38
14 2 0.08
15 3 0.12
16 10 0.42
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (14 bp):
ACAAAACCCCCCAC
Found at i:3311 original size:15 final size:15
Alignment explanation
Indices: 3279--3327 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
3269 GACACACCCA
3279 CCCAC-CAACAAAACCC
1 CCCACACAA-AAAA-CC
3295 CCCACACAAAAAACC
1 CCCACACAAAAAACC
*
3310 CCCCCAC-AAAAACC
1 CCCACACAAAAAACC
3324 CCCA
1 CCCA
3328 ACCAGAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.33
15 8 0.27
16 9 0.30
17 3 0.10
ACGTcount: A:0.45, C:0.55, G:0.00, T:0.00
Consensus pattern (15 bp):
CCCACACAAAAAACC
Found at i:3312 original size:17 final size:17
Alignment explanation
Indices: 3274--3321 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
3264 TGGTGGACAC
*
3274 ACCCACCCAC-CAACAAA
1 ACCCCCCCACACAA-AAA
3291 A-CCCCCCACACAAAAA
1 ACCCCCCCACACAAAAA
3307 ACCCCCCCACA-AAAA
1 ACCCCCCCACACAAAA
3322 CCCCCAACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (17 bp):
ACCCCCCCACACAAAAA
Found at i:11649 original size:101 final size:100
Alignment explanation
Indices: 11459--11655 Score: 288
Period size: 101 Copynumber: 2.0 Consensus size: 100
11449 CTAAACTTTG
* *
11459 TCCTTTCACTTTTCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGT
1 TCCTTTCACCTTTCAGTCCTCAAAGAGTAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGT
11524 GGCACCTTCTAGTCCTCAAAGAGCAAGACGCTCTC
66 GGCACCTTCTAGTCCTCAAAGAGCAAGACGCTCTC
* *
11559 TCCTTTCACCCTTT-AGTCCTCAAAGAGTAAGATGTTTTTTCCTTTTAAAAGCCCACACAAGTTG
1 TCCTTTCA-CCTTTCAGTCCTCAAAGAGTAAGACGTCTTTTCCTTTT-AAAGCCCACACAAGTTG
** * * *
11623 GTGGCATTTTTTTGTCCTCAAAGAGCAGGACGC
64 GTGGCACCTTCTAGTCCTCAAAGAGCAAGACGC
11656 CTTTTAAAGC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 37 0.43
101 49 0.57
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.32
Consensus pattern (100 bp):
TCCTTTCACCTTTCAGTCCTCAAAGAGTAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGT
GGCACCTTCTAGTCCTCAAAGAGCAAGACGCTCTC
Found at i:11695 original size:55 final size:56
Alignment explanation
Indices: 11599--11704 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 56
11589 GATGTTTTTT
* * ** *
11599 CCTTTTAAAAGCCCACACAAGTTGGTGGCATTTTTTTGTCCTCAAAGAGCAGGACG
1 CCTTTTAAAAGCCCACACAAGTTGGTGCCACTTCCTAGTCCTCAAAGAGCAGGACG
11655 CCTTTT-AAAGCCCACACAAGTTGGTGCCACTTCCTAGTCCTCAAAGAGCA
1 CCTTTTAAAAGCCCACACAAGTTGGTGCCACTTCCTAGTCCTCAAAGAGCA
11705 AGACACTCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 39 0.87
56 6 0.13
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (56 bp):
CCTTTTAAAAGCCCACACAAGTTGGTGCCACTTCCTAGTCCTCAAAGAGCAGGACG
Found at i:11815 original size:156 final size:156
Alignment explanation
Indices: 11465--11860 Score: 531
Period size: 156 Copynumber: 2.5 Consensus size: 156
11455 TTTGTCCTTT
*
11465 CACTTTTC-AGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CACTTTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-
* *
11529 CTTCTAGTCCTCAAAGAGCAAGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGATGT
64 CTTCTAGTCCTCAAAGAGCAAGACACTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGACG-
11594 TTTTTCCTTTTAAAAGCCCACACAAGTTGGTGG
128 ----TCCTTTTAAAAGCCCACACAAGTTGGTGG
* * *
11627 CA-TTTTTTTGTCCTCAAAGAGCAGGACG-----CCTTTTAAAGCCCACACAAGTTGGTGCCACT
1 CACTTTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
** * *
11686 TCCTAGTCCTCAAAGAGCAAGACACTCTCTCCTTTTGCCTTTTAGTCCTCAAAGAGTAGGACG-C
66 T-CTAGTCCTCAAAGAGCAAGACACTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGACGTC
11750 CTTTT-AAAGCCCACACAAGTTGGTGG
130 CTTTTAAAAGCCCACACAAGTTGGTGG
*
11776 CACTTTTCTAGTCTTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 CACTTTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-
*
11841 TTTCTAGTCCTCAAAGAGCA
64 CTTCTAGTCCTCAAAGAGCA
11861 GGACGCCTTT
Statistics
Matches: 209, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
149 23 0.11
150 29 0.14
155 3 0.01
156 128 0.61
157 2 0.01
161 4 0.02
162 20 0.10
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (156 bp):
CACTTTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
TCTAGTCCTCAAAGAGCAAGACACTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGACGTCC
TTTTAAAAGCCCACACAAGTTGGTGG
Found at i:11843 original size:27 final size:27
Alignment explanation
Indices: 11813--11898 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
11803 CGCCTTTTCC
11813 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * * * ** ** *
11840 TTTTCTAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACA-AGTTGGTGGCA
*
11868 TTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
11895 TTTT
1 TTTT
11899 TAAGTCCTCA
Statistics
Matches: 36, Mismatches: 22, Indels: 2
0.60 0.37 0.03
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:11869 original size:61 final size:61
Alignment explanation
Indices: 11749--12109 Score: 361
Period size: 61 Copynumber: 6.0 Consensus size: 61
11739 GAGTAGGACG
*
11749 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCTTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
11811 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
11871 -C----AAAGCCCACACAAGTTGGTGGCATTTT-TAAGTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCT-AGTCCTCAAAGAGCAGGACGCCTTT-T
* * * ** * * *
11927 CCTTTTGAAGACCACTA-GAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATG--TTTT
1 CCTTTTAAAGCCCAC-ACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * ** * * ** *
11986 CTCTTTGCAAAGCCCACACAGGTTGGTGGCACATTCCAGTTCTCAAAGAGCAGGACATCTCTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
12049 -CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCGAAGAGCAGGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
12110 TCTTCTCTCC
Statistics
Matches: 250, Mismatches: 32, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
54 2 0.01
55 48 0.19
56 1 0.00
57 1 0.00
59 3 0.01
60 11 0.04
61 149 0.60
62 32 0.13
63 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:12070 original size:122 final size:114
Alignment explanation
Indices: 11724--12108 Score: 398
Period size: 122 Copynumber: 3.3 Consensus size: 114
11714 CTCCTTTTGC
* * * *
11724 CTTT-TAGTCCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAG-
1 CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCAAGT
* * *
11787 TCTTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
65 TC-TCAAAGAGCAGGAC-TCTCTT-CTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * *
11840 TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTAAGTC
1 CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAAGTT
* * * *
11905 CTCAAAGAGCAGGATGCTTTCTCCTTTTGAAGACCACTA-GAGTTGGTGGCA
66 CTCAAAGAGCAGGA--CTCTCTTCTTTTAAAGCCCAC-ACGAGTTGGTGGCA
* * * * *
11956 CCTTCCAGTCCTCAAAGAGTAGGATGTTTTCTCTTTGCAAAGCCCACACAGGTTGGTGGCACATT
1 CTTTCTAGTCCTCAAAGAGCAGGATG----C-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTT
*
12021 CCAGTTCTCAAAGAGCAGGACATCTCTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
60 CAAGTTCTCAAAGAGCAGGAC-TCTCTTCTTTT-AAAGCCCACACGAGTTGGTGGCA
* *
12078 CTTTTTAGTCCTCGAAGAGCAGGATGCCTTT
1 CTTTCTAGTCCTCAAAGAGCAGGATGCCTTT
12109 TTCTTCTCTC
Statistics
Matches: 221, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
116 65 0.29
117 56 0.25
118 2 0.01
120 2 0.01
121 14 0.06
122 82 0.37
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (114 bp):
CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAAGTT
CTCAAAGAGCAGGACTCTCTTCTTTTAAAGCCCACACGAGTTGGTGGCA
Found at i:12222 original size:42 final size:42
Alignment explanation
Indices: 12120--12377 Score: 141
Period size: 42 Copynumber: 6.3 Consensus size: 42
12110 TCTTCTCTCC
* *
12120 TTTGTCCTCAAAGAGCATGACACACTTCA-TTCCCTTCTTTTCCCT
1 TTTGTCCTCAAAGAGCAAGACACACTTCATTTTCC-TC-TTT--CT
* *
12165 TTTGCCCTCAAAGAGCAAGACGCACTTCATTTTCCTCTTTCT
1 TTTGTCCTCAAAGAGCAAGACACACTTCATTTTCCTCTTTCT
* * * * * *
12207 TTTGTCCTCAAAGAGCAGGACACATTTCGTTTTTCTTTTTTCC
1 TTTGTCCTCAAAGAGCAAGACACACTTC-ATTTTCCTCTTTCT
* ** *
12250 TTTGTCCTCGAAA-AGCAGGACGTAC-TC-TTTT--TC--AC-
1 TTTGTCCTC-AAAGAGCAAGACACACTTCATTTTCCTCTTTCT
* * * *
12285 TTTGTCCTC-AAGAAGCAA-A-ACACTTTCTTTTTCTTTTTTCC
1 TTTGTCCTCAAAG-AGCAAGACACAC-TTCATTTTCCTCTTTCT
* * *
12326 TTTGTCCTCAAGGAGCAAGAC-CTATTTCATTCT-CT-TTTCT
1 TTTGTCCTCAAAGAGCAAGACAC-ACTTCATTTTCCTCTTTCT
12366 TTTGTCCTCAAA
1 TTTGTCCTCAAA
12378 AAGTGGGACA
Statistics
Matches: 167, Mismatches: 29, Indels: 39
0.71 0.12 0.17
Matches are distributed among these distances:
33 4 0.02
34 1 0.01
35 15 0.09
36 5 0.03
38 2 0.01
40 20 0.12
41 15 0.09
42 38 0.23
43 29 0.17
44 6 0.04
45 28 0.17
46 4 0.02
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (42 bp):
TTTGTCCTCAAAGAGCAAGACACACTTCATTTTCCTCTTTCT
Found at i:12255 original size:43 final size:42
Alignment explanation
Indices: 12105--12342 Score: 165
Period size: 42 Copynumber: 5.8 Consensus size: 42
12095 AGCAGGATGC
* *
12105 CTTTTTCTTCTCTCCTTTGTCCTCAAAGAGCATGACACACTT
1 CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTT
* ** * * *
12147 CATTCCCTTCTTTTCCCTTTTGCCCTCAAAGAGCAAGACGCACTT
1 CTTTTTCTTC-TTT-CC-TTTGTCCTCAAAGAGCAGGACACACTT
* * * *
12192 CATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACACATTT
1 CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTT
* **
12234 CGTTTTTCTTTTTTCCTTTGTCCTCGAAA-AGCAGGACGTAC-T
1 C-TTTTTCTTCTTTCCTTTGTCCTC-AAAGAGCAGGACACACTT
* *
12276 C--TTT-TTC---ACTTTGTCCTC-AAGAAGCA--AAACACTTT
1 CTTTTTCTTCTTTCCTTTGTCCTCAAAG-AGCAGGACACAC-TT
* *
12311 CTTTTTCTTTTTTCCTTTGTCCTCAAGGAGCA
1 CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCA
12343 AGACCTATTT
Statistics
Matches: 150, Mismatches: 30, Indels: 33
0.70 0.14 0.15
Matches are distributed among these distances:
33 5 0.03
35 16 0.11
37 3 0.02
38 4 0.03
39 3 0.02
41 14 0.09
42 35 0.23
43 31 0.21
44 8 0.05
45 31 0.21
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (42 bp):
CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTT
Found at i:13031 original size:20 final size:20
Alignment explanation
Indices: 13006--13056 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
12996 CCCGGATGCG
*
13006 TCGATACATT-TTGCATTGTA
1 TCGATACATTGCT-CATTGTA
13026 TCGATACATTGCTCATTGTA
1 TCGATACATTGCTCATTGTA
13046 TCGATACATTG
1 TCGATACATTG
13057 TATCGATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (20 bp):
TCGATACATTGCTCATTGTA
Found at i:13055 original size:13 final size:13
Alignment explanation
Indices: 13039--13068 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
13029 ATACATTGCT
13039 CATTGTATCGATA
1 CATTGTATCGATA
13052 CATTGTATCGATA
1 CATTGTATCGATA
13065 CATT
1 CATT
13069 CTGGATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:13108 original size:20 final size:20
Alignment explanation
Indices: 13083--13137 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
13073 ATTTACCTAG
*
13083 ATGTATCGATACATTTTATA
1 ATGTATCGATACATTTTACA
13103 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
13123 ATGTATCGATACATT
1 ATGTATCGATACATT
13138 CAGGCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:13109 original size:82 final size:82
Alignment explanation
Indices: 12972--13137 Score: 226
Period size: 82 Copynumber: 2.0 Consensus size: 82
12962 TTTTCATAAT
* * * * *
12972 TTGTATCGATACATTCTGGGTTTACCCGGATGCGTCGATACATTTTGCATTGTATCGATACATTG
1 TTGTATCGATACATTCTGGATTTACCCAGATGCATCGATACATTTTACAATGTATCGATACATT-
*
13037 CT-CATTGTATCGATACA
65 CTACAATGTATCGATACA
* * * *
13054 TTGTATCGATACATTCTGGATTTACCTAGATGTATCGATACATTTTATAATGTATCGATACATTT
1 TTGTATCGATACATTCTGGATTTACCCAGATGCATCGATACATTTTACAATGTATCGATACATTC
13119 TACAATGTATCGATACA
66 TACAATGTATCGATACA
13136 TT
1 TT
13138 CAGGCATTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 1 0.01
82 72 0.99
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (82 bp):
TTGTATCGATACATTCTGGATTTACCCAGATGCATCGATACATTTTACAATGTATCGATACATTC
TACAATGTATCGATACA
Found at i:15035 original size:51 final size:51
Alignment explanation
Indices: 14975--15143 Score: 241
Period size: 51 Copynumber: 3.3 Consensus size: 51
14965 ATTTTTCATC
* * * *
14975 TCGGGGATACTCCAAC-CCTGGTTTTATTTCCACAACATCAATTTTCCACAA
1 TCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTTCCATAA
* * *
15026 TCGGAGATACTCCAACTCCGATTTTATTTCTAAAACACCTATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
*
15077 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
*
15128 TCAGGGATACTCCAAC
1 TCGGGGATACTCCAAC
15144 CTCGGTATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 103 0.98
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:15194 original size:29 final size:28
Alignment explanation
Indices: 15131--15201 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
15121 TTCATAATCA
* *
15131 GGGATACTCCAACCTCGGTATTTCTTTG
1 GGGATACTCCAACCTCGGTATTTCGTGG
** *
15159 ACGATACTCCAACCTCGTTATTTTCGTGG
1 GGGATACTCCAACCTCGGTA-TTTCGTGG
15188 GGGATACTCCAACC
1 GGGATACTCCAACC
15202 CTAGCTTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (28 bp):
GGGATACTCCAACCTCGGTATTTCGTGG
Found at i:15297 original size:79 final size:80
Alignment explanation
Indices: 15161--15329 Score: 209
Period size: 79 Copynumber: 2.1 Consensus size: 80
15151 TTTCTTTGAC
* * * * *
15161 GATACTCCAACCTCGTTATTTTCGTGGGGGATACTCCAACCCTAGCTTTATTCCTAAAATATTGA
1 GATACTCCAACCTCGTTATTTCCGTCGGGGATACTCCAACCCTAGCCTTATTCCTAAAACATCGA
15226 -TTTCTCACAATCGAG
66 TTTTC-CACAATCGAG
* * *
15241 GATACTCCAACGC-CGTTATTTCCG-CGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCG
1 GATACTCCAAC-CTCGTTATTTCCGTCGGGGATACTCCAACCCTAGCCTTATTCCTAAAACATCG
* *
15304 ATTTTCCATAATCGGG
65 ATTTTCCACAATCGAG
15320 GATACTCCAA
1 GATACTCCAA
15330 TCCCGACTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 51 0.66
80 25 0.32
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (80 bp):
GATACTCCAACCTCGTTATTTCCGTCGGGGATACTCCAACCCTAGCCTTATTCCTAAAACATCGA
TTTTCCACAATCGAG
Found at i:15342 original size:51 final size:50
Alignment explanation
Indices: 15265--15383 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 50
15255 GTTATTTCCG
* * *
15265 CGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTT-TCCATAAT
1 CGGGGATACTCCAACCC-GACCTTATTCCTAAAGCATCGATTTCT-CACAAT
* * *
15316 CGGGGATACTCCAATCCCGACTTTATTCCTAAAGTATTGATTTCTCACAAT
1 CGGGGATACTCCAA-CCCGACCTTATTCCTAAAGCATCGATTTCTCACAAT
15367 CGGGGATACTCCAACCC
1 CGGGGATACTCCAACCC
15384 CGTTATTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
50 3 0.05
51 53 0.88
52 4 0.07
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (50 bp):
CGGGGATACTCCAACCCGACCTTATTCCTAAAGCATCGATTTCTCACAAT
Found at i:15401 original size:79 final size:79
Alignment explanation
Indices: 15317--15464 Score: 210
Period size: 79 Copynumber: 1.9 Consensus size: 79
15307 TTCCATAATC
* * * *
15317 GGGGATACTCCAATCCC-GACTTTATTCCTAAAGTATTGA-TTTCTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCAG-CCTTATTCCTAAAGCATCGATTTTC-CACAATCGGGGATACTCCA
15380 ACCCCGTTATTTTCAT
64 ACCCCGTTATTTTCAT
* *
15396 GGGGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGCCTTATTCCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAAC
15461 CCCG
66 CCCG
15465 GCTTTATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
79 56 0.92
80 5 0.08
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (79 bp):
GGGGATACTCCAACCCCAGCCTTATTCCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAAC
CCCGTTATTTTCAT
Found at i:15420 original size:130 final size:129
Alignment explanation
Indices: 15187--15512 Score: 474
Period size: 130 Copynumber: 2.5 Consensus size: 129
15177 TATTTTCGTG
* * *
15187 GGGGATACTCCAACCCTAGCTTTATTCCTAAAATATTGATTTCTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCGA-CTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAAC
* * ** *
15252 GCCGTTATTTCCGCGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTTTCCATAATC
65 CCCGTTATTTCCACGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATC
15317 GGGGATACTCCAATCCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAA-CCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAAC
* * *
15382 CCCGTTATTTTCATGGGGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATC
65 CCCGTTATTTCCACGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATC
* * * *
15447 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAG-ATTAATTTCTCACAATCGGGGATACTTCAA
1 GGGGATACTCCAA-CCCGACTTTA-TTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAA
15511 CC
64 CC
15513 TCGACCTTAT
Statistics
Matches: 178, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
130 166 0.93
131 12 0.07
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (129 bp):
GGGGATACTCCAACCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAACC
CCGTTATTTCCACGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATC
Found at i:15462 original size:51 final size:51
Alignment explanation
Indices: 15396--15608 Score: 220
Period size: 51 Copynumber: 4.2 Consensus size: 51
15386 TTATTTTCAT
* *
15396 GGGGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTC-CACAATC
1 GGGGATACTCCAACCCC-GCCTTATTTCTAAAGCATCGAATTTCTCACAATC
* * *
15447 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAG-AT-TAATTTCTCACAATC
1 GGGGATACTCCAACCCC-GCCTTATTT-CTAAAGCATCGAATTTCTCACAATC
* * *
15498 GGGGATACTTCAACCTCGACCTTATTTCTAAATCATC-AATTTCTCACAATC
1 GGGGATACTCCAACCCCG-CCTTATTTCTAAAGCATCGAATTTCTCACAATC
* * * * *
15549 GAGGATACTTCAACCCTTGCCTTATTTCTAAATCATCG-ATTTTTCACAATC
1 GGGGATACTCCAACCC-CGCCTTATTTCTAAAGCATCGAATTTCTCACAATC
*
15600 GAGGATACT
1 GGGGATACT
15609 ATAAACCTGT
Statistics
Matches: 140, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
50 10 0.07
51 124 0.89
52 6 0.04
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGCCTTATTTCTAAAGCATCGAATTTCTCACAATC
Found at i:15574 original size:102 final size:102
Alignment explanation
Indices: 15415--15608 Score: 246
Period size: 102 Copynumber: 1.9 Consensus size: 102
15405 CTAACCCCAG
* * *
15415 CCTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAA
1 CCTTATTTCTAAAGCATCAATTTTCCACAATCGAGGATACTCCAACCCCGGCCTTATTTCCAAAA
* * *
15480 GATTAATTTCTCACAATCGGGGATACTTCAACCTCGA
66 CATCAATTTCTCACAATCGAGGATACTTCAACCTCGA
* * ** *
15517 CCTTATTTCTAAATCATCAA-TTTCTCACAATCGAGGATACTTCAACCCTTGCCTTATTTCTAAA
1 CCTTATTTCTAAAGCATCAATTTTC-CACAATCGAGGATACTCCAACCCCGGCCTTATTTCCAAA
* * *
15581 TCATCGATTTTTCACAATCGAGGATACT
65 ACATCAATTTCTCACAATCGAGGATACT
15609 ATAAACCTGT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 4 0.05
102 73 0.95
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (102 bp):
CCTTATTTCTAAAGCATCAATTTTCCACAATCGAGGATACTCCAACCCCGGCCTTATTTCCAAAA
CATCAATTTCTCACAATCGAGGATACTTCAACCTCGA
Found at i:15671 original size:232 final size:232
Alignment explanation
Indices: 15265--15694 Score: 523
Period size: 232 Copynumber: 1.9 Consensus size: 232
15255 GTTATTTCCG
* * * *
15265 CGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTTTCCATAATCGGGGATACTCCAA
1 CGGGGATACTCCAACCCTGACCTTATTTCTAAAGCATCAATTTTCCACAATCGAGGATACTCCAA
* * * * *
15330 TCCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCA
66 TCCCGACCTTATTCCTAAAGTATCGATTTCTCACAATCGAGGATACTACAAACCCGTTATTTTCA
* * * *
15395 TGGGGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAA
131 TGGGGATACTCCAACCCCAACCTTATTTCTAAAACATCGATTTTCCACAATCAGGGATACTCCAA
15460 CCCCGGCTTTATTTCCAAAAGATTAATTTCTCACAAT
196 CCCCGGCTTTATTTCCAAAAGATTAATTTCTCACAAT
* * *
15497 CGGGGATACTTCAA-CCTCGACCTTATTTCTAAATCATCAA-TTTCTCACAATCGAGGATACTTC
1 CGGGGATACTCCAACCCT-GACCTTATTTCTAAAGCATCAATTTTC-CACAATCGAGGATACTCC
* * * *
15560 AA-CCCTTG-CCTTATTTCTAAA-TCATCGATTTTTCACAATCGAGGATACTATAAACCTGTTAT
64 AATCCC--GACCTTATTCCTAAAGT-ATCGATTTCTCACAATCGAGGATACTACAAACCCGTTAT
** * * *
15622 TTTCGA-GGGGATACTCCAACCCCAATTTTATTT-TCAAAATATCGATTTTCTATAATCAGGGAT
126 TTTC-ATGGGGATACTCCAACCCCAACCTTATTTCT-AAAACATCGATTTTCCACAATCAGGGAT
15685 ACTCCAACCC
189 ACTCCAACCC
15695 TGTTATTTCC
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
231 12 0.07
232 152 0.92
233 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (232 bp):
CGGGGATACTCCAACCCTGACCTTATTTCTAAAGCATCAATTTTCCACAATCGAGGATACTCCAA
TCCCGACCTTATTCCTAAAGTATCGATTTCTCACAATCGAGGATACTACAAACCCGTTATTTTCA
TGGGGATACTCCAACCCCAACCTTATTTCTAAAACATCGATTTTCCACAATCAGGGATACTCCAA
CCCCGGCTTTATTTCCAAAAGATTAATTTCTCACAAT
Found at i:15748 original size:79 final size:79
Alignment explanation
Indices: 15573--15769 Score: 193
Period size: 79 Copynumber: 2.5 Consensus size: 79
15563 CCTTGCCTTA
* ** * * ** * * *
15573 TTTCTAAATCATCGATTTTTCACAATCGAGGATACTATAAACCTGTTATTTTCGAGGGGATACTC
1 TTTC-AAAACATCGATTTCCCATAATCGTGGATACTCCAACCCTGTTATTTCCGAAGGGATACTC
15638 CAACCCCAATTTTAT
65 CAACCCCAATTTTAT
* * * *
15653 TTTCAAAATATCGATTTTCTATAATCAG-GGATACTCCAACCCTGTTATTTCCGAAGGGATGCTC
1 TTTCAAAACATCGATTTCCCATAATC-GTGGATACTCCAACCCTGTTATTTCCGAAGGGATACTC
*
15717 CAACCCCGATTTTA-
65 CAACCCCAATTTTAT
*
15731 TTTCTAGAACA-CTGATTTCCCATAATCGTGGATACTCCA
1 TTTC-AAAACATC-GATTTCCCATAATCGTGGATACTCCA
15770 GCCCCGTTGT
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
78 6 0.06
79 86 0.89
80 5 0.05
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTCAAAACATCGATTTCCCATAATCGTGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCC
AACCCCAATTTTAT
Found at i:18175 original size:165 final size:161
Alignment explanation
Indices: 17887--18269 Score: 420
Period size: 165 Copynumber: 2.3 Consensus size: 161
17877 CATCATGAAC
* *** *
17887 TCCTTTTTTAAAATAC-AGTGTTTTCTACTTTGTAAATTTTTTTGAGAGGATTTTTCTCAGTTTT
1 TCCTTTTTTAAAATACGA-AGTTTTCTACTCCATAAA-TTTTTTG-GAGGATTTTTCTCAATTTT
* * * **
17951 TAATTTTAAAATTTATAAAATATTATTATTTAACTCACATTAAATCAGATTTCAAAAATTTGTTC
63 TAATTTTAAAATTCATAAAACATTATTATTTAACTCACATTAAAACAGATTTCAAAAATTAATTC
*
18016 A-TCTTCATGAGTCTTT-GAATTTTTTC-TTGAAATTT
128 AGT-TTCATAAGT-TTTAG-ATTTTTTCTTTGAAA-TT
18051 TCCTATTTTTAAAATACGAAGTTTTCTACTCCATAAATTTTTTAGGAGGATTTTTCTCAATTTTT
1 TCCT-TTTTTAAAATACGAAGTTTTCTACTCCATAAATTTTTT-GGAGGATTTTTCTCAATTTTT
* * *
18116 AATTTTTAAAATTCATAAAACATTTTTATTTAATTCACATTAAAACA-ATTTTGAAAAATTAATT
64 AA-TTTTAAAATTCATAAAACATTATTATTTAACTCACATTAAAACAGA-TTTCAAAAATTAATT
*
18180 TAGTTTCATAAGTTTTAGATTTTTTCTTTGAAATT
127 CAGTTTCATAAGTTTTAGATTTTTTCTTTGAAATT
* *
18215 CCCTTTTCTTGAAAA-ACTGAA-TTTTCTATTCCATAAATATTTTTGGAGGGATTTT
1 TCCTTTT-TT-AAAATAC-GAAGTTTTCTACTCCATAAAT-TTTTTGGA-GGATTTT
18270 CTTTGGTTTA
Statistics
Matches: 189, Mismatches: 17, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
163 3 0.02
164 71 0.38
165 113 0.60
166 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (161 bp):
TCCTTTTTTAAAATACGAAGTTTTCTACTCCATAAATTTTTTGGAGGATTTTTCTCAATTTTTAA
TTTTAAAATTCATAAAACATTATTATTTAACTCACATTAAAACAGATTTCAAAAATTAATTCAGT
TTCATAAGTTTTAGATTTTTTCTTTGAAATT
Found at i:18365 original size:20 final size:20
Alignment explanation
Indices: 18322--18370 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
18312 AACTCCCATT
*
18322 AATTTATTTTTGGAAATTTC
1 AATTTATTTTTGGAAATTTA
*
18342 AATTTATTTTAT-GAATTTTA
1 AATTTATTTT-TGGAAATTTA
18362 AATTT-TTTT
1 AATTTATTTT
18371 CTATATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 21 0.81
21 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (20 bp):
AATTTATTTTTGGAAATTTA
Found at i:19359 original size:10 final size:10
Alignment explanation
Indices: 19338--19366 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
19328 GCTGATCTTG
19338 ATGATT-TTT
1 ATGATTATTT
19347 ATGATTATTT
1 ATGATTATTT
19357 ATGATTATTT
1 ATGATTATTT
19367 CATTGTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (10 bp):
ATGATTATTT
Found at i:20983 original size:156 final size:157
Alignment explanation
Indices: 20534--21115 Score: 371
Period size: 156 Copynumber: 3.7 Consensus size: 157
20524 CAATTCCAAG
** * * * * * * * * * *
20534 GTTGTCACTGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAAGATTGTTTCA-TCCCATCAATAA
1 GTTGTCACCAGGTCCACTTTCATGCAGAAGATGGGCATTTAGGATAGGTTCACGCCCATCTATAA
* * * * * * ** *
20598 TTCTTTTTAAGTCTTTTAAGGG-TATC-AGGTACTTCTACGTCGAAGGTAT-CCTTTAAGGGCAT
66 -TCTTTTTAAGTCCTTT-AGGGTTGTCGGGGTACTTTTACGTTGAAAGTATACCCATAAAGGCAT
* ** * * * * *
20660 TTTCGTAATTTTTTAGAACTAACTCTTAG
129 TTTCGAAATTTCCTAAAACGAAGTCCTAA
** * * * * ** * * *
20689 GTTGTCACTTGGTCCACTTTTATGCTGAAGGTTGATATTTAGGGTAGGTTCATC-CCAAT-TAAA
1 GTTGTCACCAGGTCCACTTTCATGCAGAAGATGGGCATTTAGGATAGGTTCA-CGCCCATCTATA
* * * *
20752 ATTCTTTTTAAGTCCTTTAGGGTTGAT-GGGATATTTTTACGTT-AAAGGTATACCCATGAGGGC
65 A-TCTTTTTAAGTCCTTTAGGGTTG-TCGGGGTACTTTTACGTTGAAA-GTATACCCATAAAGGC
*
20815 ATTTTCGAAATTTCCTAAAATCG-AGTCCTAG
127 ATTTTCGAAATTTCCTAAAA-CGAAGTCCTAA
** * * * *
20846 GTTGTCACCAGGTCTGCTTTTATGCCGAA-ATGGGGCATTTAGGATAGGTTCA-TCCCATCTCTA
1 GTTGTCACCAGGTCCACTTTCATGCAGAAGAT-GGGCATTTAGGATAGGTTCACGCCCATCTATA
* ***
20909 GTCTTTTTAAGTCCTTTAGGGTTGTCGGGGTACTTTTACGTTGAAAGTATACTTGTAAAGGCATT
65 ATCTTTTTAAGTCCTTTAGGGTTGTCGGGGTACTTTTACGTTGAAAGTATACCCATAAAGGCATT
* ** ** *
20974 TTCGTAATTTTTTGGAACGAATTCCTAA
130 TTCGAAATTTCCTAAAACGAAGTCCTAA
* * *
21002 GTTGTCACCAGGTCCACTTTCATGGAGAAGATGGGTATTTAGGATAGTTTCACGCCCATCTATAA
1 GTTGTCACCAGGTCCACTTTCATGCAGAAGATGGGCATTTAGGATAGGTTCACGCCCATCTATAA
* ** *
21067 TCCTTTTTAAGTCCTTTAAGGG-TATC-AAGCACTTTTACGTTGAAAGTAT
66 T-CTTTTTAAGTCCTTT-AGGGTTGTCGGGGTACTTTTACGTTGAAAGTAT
21116 CCTCTAGGGG
Statistics
Matches: 338, Mismatches: 71, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
154 4 0.01
155 69 0.20
156 135 0.40
157 107 0.32
158 19 0.06
159 4 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.38
Consensus pattern (157 bp):
GTTGTCACCAGGTCCACTTTCATGCAGAAGATGGGCATTTAGGATAGGTTCACGCCCATCTATAA
TCTTTTTAAGTCCTTTAGGGTTGTCGGGGTACTTTTACGTTGAAAGTATACCCATAAAGGCATTT
TCGAAATTTCCTAAAACGAAGTCCTAA
Found at i:21105 original size:313 final size:313
Alignment explanation
Indices: 20532--21112 Score: 656
Period size: 313 Copynumber: 1.9 Consensus size: 313
20522 ACCAATTCCA
** * * * *
20532 AGGTTGTCACTGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAAGATTGTTTCATCCCATCAATA
1 AGGTTGTCACCAGGTCCGCTTTTATGCCGAAGGTGGGCATTTAAGATAGGTTCATCCCATCAATA
* * * * *
20597 ATTCTTTTTAAGTCTTTTAAGGGTATCAGGTACTTCTACGTCGAAGGTATCCTTTAAGGGCATTT
66 AGTCTTTTTAAGTCCTTTAAGGGTATCAGGTACTTCTACGTCGAAAGTATACTTTAAAGGCATTT
* * * ** * * * *
20662 TCGTAATTTTTTAGAACTAACTCTTAGGTTGTCACTTGGTCCACTTTTATGCTGAAGGTTGATAT
131 TCGTAATTTTTTAGAACGAACTCCTAAGTTGTCACCAGGTCCACTTTCATGCAGAAGATGGATAT
* * ** * *
20727 TTAGGGTAGGTTCATCCCAATTAAAATTCTTTTTAAGTCCTTTAGGGTTGATGGGATATTTTTAC
196 TTAGGATAGGTTCATCCCAATTAAAATCCTTTTTAAGTCCTTTAGGGTTGATAAGACACTTTTAC
20792 GTT-AAAGGTATACCCATGAGGGCATTTTCGAAATTTCCTAAAATCGAGTCCT
261 GTTGAAAGGTATACCCATGAGGGCATTTTCGAAATTTCCTAAAATCGAGTCCT
* * * **
20844 AGGTTGTCACCAGGTCTGCTTTTATGCCGAA-ATGGGGCATTTAGGATAGGTTCATCCCATCTCT
1 AGGTTGTCACCAGGTCCGCTTTTATGCCGAAGGT-GGGCATTTAAGATAGGTTCATCCCATCAAT
* * * *
20908 -AGTCTTTTTAAGTCCTTT-AGGGTTGTCGGGGTACTTTTACGTTGAAAGTATACTTGTAAAGGC
65 AAGTCTTTTTAAGTCCTTTAAGGG-TATC-AGGTACTTCTACGTCGAAAGTATACTT-TAAAGGC
* * *
20971 ATTTTCGTAATTTTTTGGAACGAATTCCTAAGTTGTCACCAGGTCCACTTTCATGGAGAAGATGG
127 ATTTTCGTAATTTTTTAGAACGAACTCCTAAGTTGTCACCAGGTCCACTTTCATGCAGAAGATGG
* * * *
21036 GTATTTAGGATAGTTTCA-CGCCCATCTATAATCCTTTTTAAGTCCTTTAAGGG-T-ATCAAG-C
192 ATATTTAGGATAGGTTCATC-CCAAT-TAAAATCCTTTTTAAGTCCTTT-AGGGTTGAT-AAGAC
21097 ACTTTTACGTTGAAAG
253 ACTTTTACGTTGAAAG
21113 TATCCTCTAG
Statistics
Matches: 218, Mismatches: 42, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
310 4 0.02
311 20 0.09
312 74 0.34
313 90 0.41
314 26 0.12
315 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (313 bp):
AGGTTGTCACCAGGTCCGCTTTTATGCCGAAGGTGGGCATTTAAGATAGGTTCATCCCATCAATA
AGTCTTTTTAAGTCCTTTAAGGGTATCAGGTACTTCTACGTCGAAAGTATACTTTAAAGGCATTT
TCGTAATTTTTTAGAACGAACTCCTAAGTTGTCACCAGGTCCACTTTCATGCAGAAGATGGATAT
TTAGGATAGGTTCATCCCAATTAAAATCCTTTTTAAGTCCTTTAGGGTTGATAAGACACTTTTAC
GTTGAAAGGTATACCCATGAGGGCATTTTCGAAATTTCCTAAAATCGAGTCCT
Found at i:21128 original size:156 final size:156
Alignment explanation
Indices: 20393--21129 Score: 559
Period size: 157 Copynumber: 4.7 Consensus size: 156
20383 GCTGAGTCTG
* * * * *
20393 CTTTTATGCTGAAGATAGATATTTATGATAGGTTCATCCCTTCTATAA-TCTTTTTTAAGTCTTT
1 CTTTTATGCTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATTC-TTTTTAAGTCCTT
** * * * * * *** * * *
20457 TAGGAATACCGAGATACTTTCACGTCG-AAGACATACAAATAGGGACATTTTGGTAATTTCATAG
65 TAGGGTTATC-AGGTACTTTTACGTTGAAAG-TATACCTCTAGGGGCATTTTCGTAATTTCTTAG
* ** *
20521 AACCAATTCC-AAGGTTGTCACTGGGTCCG
128 AACGAATTCCTAA-GTTGTCACCAGGTCCA
* * * * * *
20550 CTTTTATGCTGAAGGTGGGTATTTAAGATTGTTTCATCCCATCAATAATTCTTTTTAAGTCTTTT
1 CTTTTATGCTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCCTTT
* * * * * *
20615 AAGGG-TATCAGGTACTTCTACGTCGAAGGTAT-CCTTTAAGGGCATTTTCGTAATTTTTTAGAA
66 -AGGGTTATCAGGTACTTTTACGTTGAAAGTATACCTCTAGGGGCATTTTCGTAATTTCTTAGAA
* * * * **
20678 CTAACTCTTAGGTTGTCACTTGGTCCA
130 CGAATTCCTAAGTTGTCACCAGGTCCA
* * * * *
20705 CTTTTATGCTGAAGGTTGATATTTAGGGTAGGTTCATCCCAAT-TAAAATTCTTTTTAAGTCCTT
1 CTTTTATGCTGAAGATGGGTATTTAGGATAGGTTCATCCC-ATCTATAATTCTTTTTAAGTCCTT
* * * *
20769 TAGGGTTGAT-GGGATATTTTTACGTT-AAAGGTATACC-C-ATGAGGGCATTTTCGAAATTTCC
65 TAGGGTT-ATCAGG-TACTTTTACGTTGAAA-GTATACCTCTA-G-GGGCATTTTCGTAATTTCT
* * * **
20830 TAAAATCG-AGTCCTAGGTTGTCACCAGGTCTG
125 TAGAA-CGAATTCCTAAGTTGTCACCAGGTCCA
* * * *
20862 CTTTTATGCCGAA-ATGGGGCATTTAGGATAGGTTCATCCCATCTCT-AGTCTTTTTAAGTCCTT
1 CTTTTATGCTGAAGAT-GGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCCTT
* * * * ** * *
20925 TAGGGTTGTCGGGGTACTTTTACGTTGAAAGTATACTTGTAAAGGCATTTTCGTAATTTTTTGGA
65 TAGGGTTATC-AGGTACTTTTACGTTGAAAGTATACCTCTAGGGGCATTTTCGTAATTTCTTAGA
20990 ACGAATTCCTAAGTTGTCACCAGGTCCA
129 ACGAATTCCTAAGTTGTCACCAGGTCCA
* ** * * *
21018 CTTTCATGGAGAAGATGGGTATTTAGGATAGTTTCACGCCCATCTATAATCCTTTTTAAGTCCTT
1 CTTTTATGCTGAAGATGGGTATTTAGGATAGGTTCA-TCCCATCTATAATTCTTTTTAAGTCCTT
* *
21083 TAAGGG-TATCAAGCACTTTTACGTTGAAAGTAT-CCTCTAGGGGCATT
65 T-AGGGTTATCAGGTACTTTTACGTTGAAAGTATACCTCTAGGGGCATT
21130 ATCAAAATTT
Statistics
Matches: 458, Mismatches: 97, Indels: 51
0.76 0.16 0.08
Matches are distributed among these distances:
154 4 0.01
155 104 0.23
156 152 0.33
157 168 0.37
158 26 0.06
159 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (156 bp):
CTTTTATGCTGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCCTTT
AGGGTTATCAGGTACTTTTACGTTGAAAGTATACCTCTAGGGGCATTTTCGTAATTTCTTAGAAC
GAATTCCTAAGTTGTCACCAGGTCCA
Found at i:25015 original size:21 final size:20
Alignment explanation
Indices: 24989--25034 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
24979 GCTGAAATAA
24989 AAAAAAAAGAGAAAAGAAAAG
1 AAAAAAAAGAGAAAA-AAAAG
* *
25010 AAAAAAAAGTGAAAAAATAG
1 AAAAAAAAGAGAAAAAAAAG
25030 AAAAA
1 AAAAA
25035 GTGAAGCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAAAAGAGAAAAAAAAG
Found at i:26622 original size:69 final size:69
Alignment explanation
Indices: 26549--26701 Score: 234
Period size: 69 Copynumber: 2.2 Consensus size: 69
26539 TTTTCACAAT
* * * *
26549 TTGTATCAATACATTGTTCATTGTATCGATACATTCTAGGTTTACCCAGATGTATCGATGCATTT
1 TTGTATCAATACATTGCTCAATGTATCGATACATTCTAGATTTACCCAGATGTATCGATACATTT
*
26614 TGCA
66 TACA
*
26618 TTGTATCGATACATTGCTCAATGTATCGATACATTCTAGATTTACCCAGATGTATCGATACATTT
1 TTGTATCAATACATTGCTCAATGTATCGATACATTCTAGATTTACCCAGATGTATCGATACATTT
26683 TACA
66 TACA
* *
26687 ATGTATCTATACATT
1 TTGTATCAATACATT
26702 CAGGCATTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (69 bp):
TTGTATCAATACATTGCTCAATGTATCGATACATTCTAGATTTACCCAGATGTATCGATACATTT
TACA
Found at i:26692 original size:20 final size:20
Alignment explanation
Indices: 26598--26701 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
26588 GTTTACCCAG
* *
26598 ATGTATCGATGCATTTTGCA
1 ATGTATCGATACATTTTACA
* *
26618 TTGTATCGATACATTGCT-CA
1 ATGTATCGATACATT-TTACA
26638 ATGTATCGATACATTCTAGATTTACCCA
1 ATGTATCGATACA---T---TTTA--CA
26666 GATGTATCGATACATTTTACA
1 -ATGTATCGATACATTTTACA
*
26687 ATGTATCTATACATT
1 ATGTATCGATACATT
26702 CAGGCATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
20 41 0.61
21 3 0.04
23 5 0.07
25 1 0.01
26 2 0.03
28 2 0.03
29 13 0.19
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:27516 original size:52 final size:50
Alignment explanation
Indices: 27360--27516 Score: 206
Period size: 51 Copynumber: 3.1 Consensus size: 50
27350 TAACCCCCGG
* * *
27360 TTTTATTTCCACAACATCAATTTTCCATAATCGGAGATAATCCAACTCTGA
1 TTTTATTTCCAAAACACCAATTTTCCATAATCGG-GATACTCCAACTCTGA
*
27411 TTTTATTTCTAAAACACCAATTTTCCATAATCGGGGATACTCCAACTCTGA
1 TTTTATTTCCAAAACACCAATTTTCCATAATC-GGGATACTCCAACTCTGA
* * * *
27462 TTTTATTTCCAAAATTACCAATTTTTCACAATCGGGATACTCCAACCCTGGA
1 TTTTATTTCCAAAA-CACCAATTTTCCATAATCGGGATACTCCAACTCT-GA
27514 TTT
1 TTT
27517 CATTGGGGAT
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
51 72 0.77
52 22 0.23
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (50 bp):
TTTTATTTCCAAAACACCAATTTTCCATAATCGGGATACTCCAACTCTGA
Found at i:27546 original size:29 final size:26
Alignment explanation
Indices: 27495--27568 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 26
27485 TTTCACAATC
*
27495 GGGATACTCCAACCCTGGATTTC-ATTG
1 GGGATACTCCAACCCCGGATTTCGA--G
*
27522 GGGATACTCCAACCCCGTTATTTTCGAG
1 GGGATACTCCAACCCCG-GA-TTTCGAG
*
27550 GAGGATACTCCAACTCCGG
1 G-GGATACTCCAACCCCGG
27569 CTTTATTCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 16 0.41
28 3 0.08
29 19 0.49
30 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (26 bp):
GGGATACTCCAACCCCGGATTTCGAG
Found at i:27657 original size:31 final size:28
Alignment explanation
Indices: 27600--27657 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
27590 TTATCACAAT
*
27600 CGAGGATACTCCAACCCCGTTATTTCTG
1 CGAGGATACTCCAACCCCCTTATTTCTG
27628 CGAGGATACTCCAACTCCGGCCTTATTTCT
1 CGAGGATACTCCAAC-CC--CCTTATTTCT
27658 AAAGCATCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.58
29 2 0.08
31 9 0.35
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.29
Consensus pattern (28 bp):
CGAGGATACTCCAACCCCCTTATTTCTG
Found at i:27660 original size:79 final size:80
Alignment explanation
Indices: 27523--27695 Score: 235
Period size: 79 Copynumber: 2.2 Consensus size: 80
27513 ATTTCATTGG
* * * *
27523 GGATACTCCAACCCCGTTATTTTCGAGGAGGATACTCCAACTCCGGCTTTATTCCTAAAATATTG
1 GGATACTCCAACCCCGTTATTTTCGACGAGGATACTCCAACTCCGGCCTTATTCCTAAAACATCG
27588 ATTTAT-CACAATCGA
66 ATTT-TCCACAATCGA
* *
27603 GGATACTCCAACCCCGTTA-TTTCTG-CGAGGATACTCCAACTCCGGCCTTATTTCTAAAGCATC
1 GGATACTCCAACCCCGTTATTTTC-GACGAGGATACTCCAACTCCGGCCTTATTCCTAAAACATC
* *
27666 GATTTTCCATAATCGG
65 GATTTTCCACAATCGA
27682 GGATACTCCAACCC
1 GGATACTCCAACCC
27696 GGCTTTATTC
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
78 1 0.01
79 62 0.75
80 20 0.24
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (80 bp):
GGATACTCCAACCCCGTTATTTTCGACGAGGATACTCCAACTCCGGCCTTATTCCTAAAACATCG
ATTTTCCACAATCGA
Found at i:27710 original size:50 final size:50
Alignment explanation
Indices: 27631--27745 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
27621 ATTTCTGCGA
* * *
27631 GGATACTCCAACTCCGGCCTTATTTCTAAAGCATCGATTT-TCCATAATCGG
1 GGATACTCCAAC-CCGGCCTTATTCCTAAAACATCGATTTCT-CATAATCAG
* * *
27682 GGATACTCCAACCCGGCTTTATTCCTAAAATATTGATTTCTCATAATCAG
1 GGATACTCCAACCCGGCCTTATTCCTAAAACATCGATTTCTCATAATCAG
*
27732 GGATACTCAAACCC
1 GGATACTCCAACCC
27746 TATTATTTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
50 43 0.77
51 13 0.23
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (50 bp):
GGATACTCCAACCCGGCCTTATTCCTAAAACATCGATTTCTCATAATCAG
Found at i:27712 original size:129 final size:129
Alignment explanation
Indices: 27550--27877 Score: 473
Period size: 129 Copynumber: 2.5 Consensus size: 129
27540 TATTTTCGAG
*
27550 GAGGATACTCCAACTCCGGCTTTATTCCTAAAATATTGATTTATCACAATCGAGGATACTCCAAC
1 GAGGATACTCCAAC-CCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGAGGATACTCCAAC
* * *
27615 CCCGTTATTTCTGCGAGGATACTCCAACTCCGGCCTTATTTCTAAAGCATCGATTTTCCATAATC
65 CCCGTTATTTCTGCGAGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATC
* * *
27680 GGGGATACTCCAACCCGGCTTTATTCCTAAAATATTGATTTCTCATAATC-AGGGATACTCAAAC
1 GAGGATACTCCAACCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGA-GGATACTCCAAC
** *
27744 CCTATTATTTCTGCGGGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATC
65 CCCGTTATTTCTGCGAGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATC
* * *
27809 GAGGATACTCCAACCTCGGCTTTATT-TTCAAAATATTAATTTCTCACAATCCG-GGATACTTCA
1 GAGGATACTCCAACC-CGGCTTTATTCCT-AAAATATTGATTTCTCACAAT-CGAGGATACTCCA
27872 ACCCCG
63 ACCCCG
27878 ACCTTATTTC
Statistics
Matches: 175, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
128 1 0.01
129 119 0.68
130 54 0.31
131 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (129 bp):
GAGGATACTCCAACCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGAGGATACTCCAACC
CCGTTATTTCTGCGAGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATC
Found at i:27815 original size:79 final size:78
Alignment explanation
Indices: 27679--27823 Score: 177
Period size: 79 Copynumber: 1.8 Consensus size: 78
27669 TTTCCATAAT
* * * * *
27679 CGGGGATACTCCAACCCGGCTTTATTCCTAAAATATTGATTTCTCATAATCAGGGATACTCAAAC
1 CGGGGATACTCCAACCCGACCTTATTCCTAAAACATCGATTTCTCACAATCAGGGATACTCAAAC
27744 CCTATTATTTCTG
66 CCTATTATTTCTG
* * *
27757 CGGGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTT-TCCACAATC-GAGGATACTCC
1 CGGGGATACTCCAA-CCCGACCTTATTCCTAAAACATCGATTTCT-CACAATCAG-GGATACTCA
27820 AACC
63 AACC
27824 TCGGCTTTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 16 0.29
79 40 0.71
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCGACCTTATTCCTAAAACATCGATTTCTCACAATCAGGGATACTCAAAC
CCTATTATTTCTG
Found at i:27857 original size:51 final size:51
Alignment explanation
Indices: 27760--27975 Score: 251
Period size: 51 Copynumber: 4.3 Consensus size: 51
27750 ATTTCTGCGG
* * *
27760 GGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTT-TCCACAATCGA
1 GGATACTCCAACCTCGGCCTTATTTCTAAATCATCGATTTCT-CACAATCGA
* * **
27811 GGATACTCCAACCTCGGCTTTATTTTCAAAAT-ATTAATTTCTCACAATCCG-
1 GGATACTCCAACCTCGGCCTTA-TTTCTAAATCATCGATTTCTCACAAT-CGA
* * * *
27862 GGATACTTCAACCCCGACCTTATTTCTAAATCATCGATTTCTCACAATCGG
1 GGATACTCCAACCTCGGCCTTATTTCTAAATCATCGATTTCTCACAATCGA
* **
27913 GGATACTTCAACCTTTGCCTTATTTCTAAATCATCGATTT-TCACAATCGA
1 GGATACTCCAACCTCGGCCTTATTTCTAAATCATCGATTTCTCACAATCGA
27963 GGATACTCCAACC
1 GGATACTCCAACC
27976 CCGTTATTTT
Statistics
Matches: 140, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
50 31 0.22
51 99 0.71
52 10 0.07
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACCTCGGCCTTATTTCTAAATCATCGATTTCTCACAATCGA
Found at i:27936 original size:102 final size:100
Alignment explanation
Indices: 27759--27978 Score: 291
Period size: 102 Copynumber: 2.2 Consensus size: 100
27749 TATTTCTGCG
27759 GGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATCGAGGATACTCCAACC
1 GGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATCGAGGATACTCCAACC
* *
27824 TCGGCTTTATTTTCAAAAT-ATTAATTTCTCACAATCC
66 TCGGCCTTA-TTTCAAAATCATCAATTT-TCACAAT-C
* * * *
27861 GGGATACTTCAACCCCGACCTTATTTCTAAATCATCGA-TTTCTCACAATCGGGGATACTTCAAC
1 GGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTC-CACAATCGAGGATACTCCAAC
** * *
27925 CTTTGCCTTATTTCTAAATCATCGATTTTCACAATC
65 CTCGGCCTTATTTCAAAATCATCAATTTTCACAATC
27961 GAGGATACTCCAACCCCG
1 G-GGATACTCCAACCCCG
27979 TTATTTTCGA
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
100 2 0.02
101 34 0.33
102 68 0.65
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (100 bp):
GGGATACTCCAACCCCGACCTTATTTCTAAAGCATCGATTTTCCACAATCGAGGATACTCCAACC
TCGGCCTTATTTCAAAATCATCAATTTTCACAATC
Found at i:28082 original size:79 final size:79
Alignment explanation
Indices: 27963--28138 Score: 226
Period size: 79 Copynumber: 2.2 Consensus size: 79
27953 TCACAATCGA
* * * * * *
27963 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCGATTTTATTTTCAAAATATCGA
1 GGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGA
* **
28028 TTTTCTTTAATCAG
66 TTTCCCATAATCAG
** *
28042 GGATACTCTAACCTTGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAGAACACCGA
1 GGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGA
*
28107 TTTCCCATAATCGG
66 TTTCCCATAATCAG
*
28121 GGATACTCTAGCCCCGTT
1 GGATACTCTAACCCCGTT
28139 GTTATCTCCC
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (79 bp):
GGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGA
TTTCCCATAATCAG
Found at i:41711 original size:101 final size:100
Alignment explanation
Indices: 41521--41717 Score: 288
Period size: 101 Copynumber: 2.0 Consensus size: 100
41511 CTAAACTTTG
* *
41521 TCCTTTCACTTTTCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGT
1 TCCTTTCACCTTTCAGTCCTCAAAGAGTAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGT
41586 GGCACCTTCTAGTCCTCAAAGAGCAAGACGCTCTC
66 GGCACCTTCTAGTCCTCAAAGAGCAAGACGCTCTC
* *
41621 TCCTTTCACCCTTT-AGTCCTCAAAGAGTAAGATGTTTTTTCCTTTTAAAAGCCCACACAAGTTG
1 TCCTTTCA-CCTTTCAGTCCTCAAAGAGTAAGACGTCTTTTCCTTTT-AAAGCCCACACAAGTTG
** * * *
41685 GTGGCATTTTTTTGTCCTCAAAGAGCAGGACGC
64 GTGGCACCTTCTAGTCCTCAAAGAGCAAGACGC
41718 CTTTTAAAGC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 37 0.43
101 49 0.57
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.32
Consensus pattern (100 bp):
TCCTTTCACCTTTCAGTCCTCAAAGAGTAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGT
GGCACCTTCTAGTCCTCAAAGAGCAAGACGCTCTC
Found at i:41877 original size:156 final size:156
Alignment explanation
Indices: 41527--41920 Score: 518
Period size: 156 Copynumber: 2.5 Consensus size: 156
41517 TTTGTCCTTT
*
41527 CACTTTTC-AGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CACTTTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-
* * *
41591 CTTCTAGTCCTCAAAGAGCAAGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGATGT
64 CTTCTAGTCCTCAAAGAGAAAGACACTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGACG-
41656 TTTTTCCTTTTAAAAGCCCACACAAGTTGGTGG
128 ----TCCTTTTAAAAGCCCACACAAGTTGGTGG
* * *
41689 CA-TTTTTTTGTCCTCAAAGAGCAGGACG-----CCTTTTAAAGCCCACACAAGTTGGTGCCACT
1 CACTTTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
** * *
41748 TCCTAGTCCTCAAAGAGAAAGACACTCTCTCCTTTTGCCTTTTAGTCCTCAAAGAGTAGGACG-C
66 T-CTAGTCCTCAAAGAGAAAGACACTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGACGTC
41812 CTTTT-AAAGCCCACACAAGTTGGTGG
130 CTTTTAAAAGCCCACACAAGTTGGTGG
*
41838 CACTTTTCTAGTCTTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 CACTTTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-
*
41903 TTTCTAGTCCTCAAAGAG
64 CTTCTAGTCCTCAAAGAG
41921 CAGGACGCCT
Statistics
Matches: 206, Mismatches: 16, Indels: 26
0.83 0.06 0.10
Matches are distributed among these distances:
149 23 0.11
150 29 0.14
155 3 0.01
156 125 0.61
157 2 0.01
161 4 0.02
162 20 0.10
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (156 bp):
CACTTTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
TCTAGTCCTCAAAGAGAAAGACACTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGTAAGACGTCC
TTTTAAAAGCCCACACAAGTTGGTGG
Found at i:41905 original size:27 final size:27
Alignment explanation
Indices: 41875--41960 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
41865 CGCCTTTTCC
41875 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * * * ** ** *
41902 TTTTCTAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACA-AGTTGGTGGCA
*
41930 TTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
41957 TTTT
1 TTTT
41961 TAAGTCCTCA
Statistics
Matches: 36, Mismatches: 22, Indels: 2
0.60 0.37 0.03
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:41931 original size:61 final size:61
Alignment explanation
Indices: 41811--42171 Score: 361
Period size: 61 Copynumber: 6.0 Consensus size: 61
41801 GAGTAGGACG
*
41811 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCTTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
41873 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
41933 -C----AAAGCCCACACAAGTTGGTGGCATTTT-TAAGTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCT-AGTCCTCAAAGAGCAGGACGCCTTT-T
* * * ** * * *
41989 CCTTTTGAAGACCACTA-GAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATG--TTTT
1 CCTTTTAAAGCCCAC-ACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * ** * * ** *
42048 CTCTTTGCAAAGCCCACACAGGTTGGTGGCACATTCCAGTTCTCAAAGAGCAGGACATCTCTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
42111 -CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCGAAGAGCAGGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
42172 TCTTCTCTCC
Statistics
Matches: 250, Mismatches: 32, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
54 2 0.01
55 48 0.19
56 1 0.00
57 1 0.00
59 3 0.01
60 11 0.04
61 149 0.60
62 32 0.13
63 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:42132 original size:122 final size:114
Alignment explanation
Indices: 41786--42170 Score: 398
Period size: 122 Copynumber: 3.3 Consensus size: 114
41776 CTCCTTTTGC
* * * *
41786 CTTT-TAGTCCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAG-
1 CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCAAGT
* * *
41849 TCTTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
65 TC-TCAAAGAGCAGGAC-TCTCTT-CTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * *
41902 TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTAAGTC
1 CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAAGTT
* * * *
41967 CTCAAAGAGCAGGATGCTTTCTCCTTTTGAAGACCACTA-GAGTTGGTGGCA
66 CTCAAAGAGCAGGA--CTCTCTTCTTTTAAAGCCCAC-ACGAGTTGGTGGCA
* * * * *
42018 CCTTCCAGTCCTCAAAGAGTAGGATGTTTTCTCTTTGCAAAGCCCACACAGGTTGGTGGCACATT
1 CTTTCTAGTCCTCAAAGAGCAGGATG----C-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTT
*
42083 CCAGTTCTCAAAGAGCAGGACATCTCTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
60 CAAGTTCTCAAAGAGCAGGAC-TCTCTTCTTTT-AAAGCCCACACGAGTTGGTGGCA
* *
42140 CTTTTTAGTCCTCGAAGAGCAGGATGCCTTT
1 CTTTCTAGTCCTCAAAGAGCAGGATGCCTTT
42171 TTCTTCTCTC
Statistics
Matches: 221, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
116 65 0.29
117 56 0.25
118 2 0.01
120 2 0.01
121 14 0.06
122 82 0.37
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (114 bp):
CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAAGTT
CTCAAAGAGCAGGACTCTCTTCTTTTAAAGCCCACACGAGTTGGTGGCA
Found at i:42284 original size:42 final size:44
Alignment explanation
Indices: 42182--42292 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 44
42172 TCTTCTCTCC
*
42182 TTTGTCCTCAAAGAGCATGACACACTTCATTCCCTTCTTTTCCCT
1 TTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTCTTTT-CCT
* * *
42227 TTTGCCCTCAAAGAGCAAGACGCACTTCATTTTCC-TC-TTT-CT
1 TTTGTCCTCAAAGAGCAAGACACACTTCA-TTCCCTTCTTTTCCT
*
42269 TTTGTCCTCAAAGAGCAGGACACA
1 TTTGTCCTCAAAGAGCAAGACACA
42293 TTTCGTTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 23 0.40
44 3 0.05
45 28 0.48
46 4 0.07
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (44 bp):
TTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTCTTTTCCT
Found at i:42317 original size:43 final size:42
Alignment explanation
Indices: 42167--42332 Score: 163
Period size: 42 Copynumber: 3.9 Consensus size: 42
42157 AGCAGGATGC
* *
42167 CTTTTTCTTCTCTCCTTTGTCCTCAAAGAGCATGACACACTT
1 CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTT
* ** * * *
42209 CATTCCCTTCTTTTCCCTTTTGCCCTCAAAGAGCAAGACGCACTT
1 CTTTTTCTTC-TTT-CC-TTTGTCCTCAAAGAGCAGGACACACTT
* * * *
42254 CATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACACATTT
1 CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTT
*
42296 CGTTTTTCTTTTTTCCTTTGTCCTCGAAA-AGCAGGAC
1 C-TTTTTCTTCTTTCCTTTGTCCTC-AAAGAGCAGGAC
42333 GTACTCTTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
42 31 0.31
43 30 0.30
44 8 0.08
45 31 0.31
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (42 bp):
CTTTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTT
Found at i:42436 original size:40 final size:41
Alignment explanation
Indices: 42336--42437 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 41
42326 GCAGGACGTA
**
42336 CTCTTTTCACTTTGTCCTCAAGAAGCAAAACACTTTCTTTTT
1 CTCTTTTC-CTTTGTCCTCAAGAAGCAAAACACTTTCTCATT
* * *
42378 CTTTTTTCCTTTGTCCTCAAGGAGCAAGAC-CTATT-TCATT
1 CTCTTTTCCTTTGTCCTCAAGAAGCAAAACACT-TTCTCATT
*
42418 CTCTTTTCTTTTGTCCTCAA
1 CTCTTTTCCTTTGTCCTCAA
42438 AAAGTGGGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 23 0.44
41 22 0.42
42 7 0.13
ACGTcount: A:0.20, C:0.26, G:0.09, T:0.45
Consensus pattern (41 bp):
CTCTTTTCCTTTGTCCTCAAGAAGCAAAACACTTTCTCATT
Found at i:43092 original size:20 final size:20
Alignment explanation
Indices: 43067--43117 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
43057 CCCGGATGCG
*
43067 TCGATACATT-TTGCATTGTA
1 TCGATACATTGCT-CATTGTA
43087 TCGATACATTGCTCATTGTA
1 TCGATACATTGCTCATTGTA
43107 TCGATACATTG
1 TCGATACATTG
43118 TATCGATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (20 bp):
TCGATACATTGCTCATTGTA
Found at i:43116 original size:13 final size:13
Alignment explanation
Indices: 43100--43129 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43090 ATACATTGCT
43100 CATTGTATCGATA
1 CATTGTATCGATA
43113 CATTGTATCGATA
1 CATTGTATCGATA
43126 CATT
1 CATT
43130 CTGGATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:43169 original size:20 final size:20
Alignment explanation
Indices: 43144--43198 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
43134 ATTTACCTAG
*
43144 ATGTATCGATACATTTTATA
1 ATGTATCGATACATTTTACA
43164 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
43184 ATGTATCGATACATT
1 ATGTATCGATACATT
43199 CAGGCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:43170 original size:82 final size:82
Alignment explanation
Indices: 43033--43198 Score: 226
Period size: 82 Copynumber: 2.0 Consensus size: 82
43023 TTTTCATAAT
* * * * *
43033 TTGTATCGATACATTCTGGGTTTACCCGGATGCGTCGATACATTTTGCATTGTATCGATACATTG
1 TTGTATCGATACATTCTGGATTTACCCAGATGCATCGATACATTTTACAATGTATCGATACATT-
*
43098 CT-CATTGTATCGATACA
65 CTACAATGTATCGATACA
* * * *
43115 TTGTATCGATACATTCTGGATTTACCTAGATGTATCGATACATTTTATAATGTATCGATACATTT
1 TTGTATCGATACATTCTGGATTTACCCAGATGCATCGATACATTTTACAATGTATCGATACATTC
43180 TACAATGTATCGATACA
66 TACAATGTATCGATACA
43197 TT
1 TT
43199 CAGGCATTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 1 0.01
82 72 0.99
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (82 bp):
TTGTATCGATACATTCTGGATTTACCCAGATGCATCGATACATTTTACAATGTATCGATACATTC
TACAATGTATCGATACA
Found at i:45194 original size:50 final size:50
Alignment explanation
Indices: 45035--45198 Score: 222
Period size: 51 Copynumber: 3.2 Consensus size: 50
45025 ATTTTTCATC
* * *
45035 TCGGGGATACTCCAAC-CCTGGTTTTATTTCCACAACATCAATTTTCCACAA
1 TCGGGGATACTCCAACTCC-GATTTTATTTCCA-AACACCAATTTTCCATAA
* * *
45086 TCGGAGATACTCCAACTCCGATTTTATTTCTAAAACACCTATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTC-CAAACACCAATTTTCCATAA
*
45137 TCGGGGATACTCCAACTCCGATTTTATTTCCAAACACCAATTTTTCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAACACCAATTTTCCATAA
*
45187 TCAGGGATACTC
1 TCGGGGATACTC
45199 AACCTCGGTA
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
50 28 0.28
51 69 0.69
52 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (50 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAACACCAATTTTCCATAA
Found at i:45355 original size:79 final size:80
Alignment explanation
Indices: 45219--45387 Score: 209
Period size: 79 Copynumber: 2.1 Consensus size: 80
45209 TTTCTTTGAC
* * * * *
45219 GATACTCCAACCTCGTTATTTTCGTGGGGGATACTCCAACCCTAGCTTTATTCCTAAAATATTGA
1 GATACTCCAACCTCGTTATTTCCGTCGGGGATACTCCAACCCTAGCCTTATTCCTAAAACATCGA
45284 -TTTCTCACAATCGAG
66 TTTTC-CACAATCGAG
* * *
45299 GATACTCCAACGC-CGTTATTTCCG-CGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCG
1 GATACTCCAAC-CTCGTTATTTCCGTCGGGGATACTCCAACCCTAGCCTTATTCCTAAAACATCG
* *
45362 ATTTTCCATAATCGGG
65 ATTTTCCACAATCGAG
45378 GATACTCCAA
1 GATACTCCAA
45388 TCCCGACTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 51 0.66
80 25 0.32
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (80 bp):
GATACTCCAACCTCGTTATTTCCGTCGGGGATACTCCAACCCTAGCCTTATTCCTAAAACATCGA
TTTTCCACAATCGAG
Found at i:45400 original size:51 final size:51
Alignment explanation
Indices: 45323--45438 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
45313 GTTATTTCCG
* * *
45323 CGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTT-TCCATAAT
1 CGGGGATACTCCAACCCTGACCTTATTCCTAAAGCATCGATTTCT-CACAAT
* * *
45374 CGGGGATACTCCAATCCC-GACTTTATTCCTAAAGTATTGATTTCTCACAAT
1 CGGGGATACTCCAA-CCCTGACCTTATTCCTAAAGCATCGATTTCTCACAAT
45425 CGGGGATACTCCAA
1 CGGGGATACTCCAA
45439 ACCCCGTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
CGGGGATACTCCAACCCTGACCTTATTCCTAAAGCATCGATTTCTCACAAT
Found at i:45506 original size:131 final size:129
Alignment explanation
Indices: 45245--45571 Score: 467
Period size: 131 Copynumber: 2.5 Consensus size: 129
45235 TATTTTCGTG
* * *
45245 GGGGATACTCCAACCCTAGCTTTATTCCTAAAATATTGATTTCTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCGA-CTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAAC
* * ** *
45310 GCCGTTATTTCCGCGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTTTCCATAATC
65 CCCGTTATTTCCACGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATC
45375 GGGGATACTCCAATCCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAAA
1 GGGGATACTCCAA-CCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCC-AA
* * *
45440 CCCCGTTATTTTCATGGGGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAAT
64 CCCCGTTATTTCCACGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAAT
45505 C
129 C
* * * *
45506 GGGGATACTCCAACCCCGGCTTTATTCCAAAAG-ATTAATTTCTCACAATCGGGGGATACTTCAA
1 GGGGATACTCCAA-CCCGACTTTATTCCTAAAGTATTGATTTCTCACAATC-GGGGATACTCCAA
45570 CC
64 CC
45572 TCGACCTTAT
Statistics
Matches: 178, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
130 74 0.42
131 104 0.58
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (129 bp):
GGGGATACTCCAACCCGACTTTATTCCTAAAGTATTGATTTCTCACAATCGGGGATACTCCAACC
CCGTTATTTCCACGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATC
Found at i:45521 original size:51 final size:51
Alignment explanation
Indices: 45455--45667 Score: 211
Period size: 51 Copynumber: 4.2 Consensus size: 51
45445 TTATTTTCAT
* *
45455 GGGGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTC-CACAATC
1 GGGGATACTCCAACCCC-GCCTTATTTCTAAAGCATCGAATTTCTCACAATC
* * * *
45506 GGGGATACTCCAACCCCGGCTTTATTCCAAAAG-AT-TAATTTCTCACAATC
1 GGGGATACTCCAACCCC-GCCTTATTTCTAAAGCATCGAATTTCTCACAATC
* * *
45556 GGGGGATACTTCAACCTCGACCTTATTTCTAAATCATC-AATTTCTCACAATC
1 -GGGGATACTCCAACCCCG-CCTTATTTCTAAAGCATCGAATTTCTCACAATC
* * * * *
45608 GAGGATACTTCAACCCTTGCCTTATTTCTAAATCATCG-ATTTTTCACAATC
1 GGGGATACTCCAACCC-CGCCTTATTTCTAAAGCATCGAATTTCTCACAATC
*
45659 GCGGATACT
1 GGGGATACT
45668 ATAAACCTGT
Statistics
Matches: 137, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
49 5 0.04
50 10 0.07
51 105 0.77
52 17 0.12
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGCCTTATTTCTAAAGCATCGAATTTCTCACAATC
Found at i:45616 original size:233 final size:231
Alignment explanation
Indices: 45324--45752 Score: 512
Period size: 233 Copynumber: 1.8 Consensus size: 231
45314 TTATTTCCGC
* * * *
45324 GGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTTTCCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCTGACCTTATTTCTAAAGCATCAATTTTCCACAATCGAGGATACTCCAA-
* * * *
45389 CCC-GACTTTATTCCTAAAGT-ATTGATTTCTCACAATCGGGGATACTCCAAACCCCGTTATTTT
65 CCCTG-CCTTATTCCTAAA-TCATCGATTTCTCACAATCGCGGATACTACAAA-CCCGTTATTTT
* * *
45452 C-ATGGGGATACTCTAACCCCAGCCTTA-TTTCTAAAGCATCGATTTTCCACAATC-GGGGATAC
127 CGA-GGGGATACTCCAACCCCAACCTTATTTTC-AAA-CATCGATTTTCCACAATCAGAGGATAC
45514 TCCAACCCCGGCTTTATTCCAAAAGATTAATTTCTCACAATCG
189 TCCAACCCCGGCTTTATTCCAAAAGATTAATTTCTCACAATCG
* * *
45557 GGGGATACTTCAA-CCTCGACCTTATTTCTAAATCATCAA-TTTCTCACAATCGAGGATACTTCA
1 GGGGATACTCCAACCCT-GACCTTATTTCTAAAGCATCAATTTTC-CACAATCGAGGATACTCCA
* * * *
45620 ACCCTTGCCTTATTTCTAAATCATCGATTTTTCACAATCGCGGATACTATAAACCTGTTATTTTC
64 ACCC-TGCCTTATTCCTAAATCATCGATTTCTCACAATCGCGGATACTACAAACCCGTTATTTTC
** * * *
45685 GAGGGGATACTCCAACCCCAATTTTATTTTCAAATATCGATTTTCTATAATCAGAGGATACTCCA
128 GAGGGGATACTCCAACCCCAACCTTATTTTCAAACATCGATTTTCCACAATCAGAGGATACTCCA
45750 ACC
193 ACC
45753 TGTTATTTCC
Statistics
Matches: 165, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
231 15 0.09
232 59 0.36
233 90 0.55
234 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (231 bp):
GGGGATACTCCAACCCTGACCTTATTTCTAAAGCATCAATTTTCCACAATCGAGGATACTCCAAC
CCTGCCTTATTCCTAAATCATCGATTTCTCACAATCGCGGATACTACAAACCCGTTATTTTCGAG
GGGATACTCCAACCCCAACCTTATTTTCAAACATCGATTTTCCACAATCAGAGGATACTCCAACC
CCGGCTTTATTCCAAAAGATTAATTTCTCACAATCG
Found at i:45813 original size:78 final size:77
Alignment explanation
Indices: 45632--45826 Score: 198
Period size: 78 Copynumber: 2.5 Consensus size: 77
45622 CCTTGCCTTA
* * * ** * *
45632 TTTCTAAATCATCGATTTTTCACAATCGCGGATACTATAAACCTGTTATTTTCGAGGGGATACTC
1 TTTC-AAA-CATCGATTTTCCATAATCGAGGATACT-CCAACCTGTTATTTCCGAAGGGATACTC
45697 CAACCCCAATTTTAT
63 CAACCCCAATTTTAT
* * *
45712 TTTCAAATATCGATTTTCTATAATCAGAGGATACTCCAACCTGTTATTTCCGAAGGGATGCTCCA
1 TTTCAAACATCGATTTTCCATAATC-GAGGATACTCCAACCTGTTATTTCCGAAGGGATACTCCA
*
45777 ACCCCGATTTTA-
65 ACCCCAATTTTAT
*
45789 TTTCTAGAACA-CTGA-TTTCCATAATCGTGGATACTCCA
1 TTTC-A-AACATC-GATTTTCCATAATCGAGGATACTCCA
45827 GCCCCGTTGT
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
77 15 0.15
78 62 0.64
79 16 0.16
80 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (77 bp):
TTTCAAACATCGATTTTCCATAATCGAGGATACTCCAACCTGTTATTTCCGAAGGGATACTCCAA
CCCCAATTTTAT
Done.