Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1210
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: 45983
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1738 original size:22 final size:23
Alignment explanation
Indices: 1713--1775 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 23
1703 ACACCACCAA
*
1713 CAACAAAACACCAAACCAAAA-C
1 CAACAAAACACCAAAACAAAACC
*
1735 CAAC-AAAC-CAAAAACAAAACC
1 CAACAAAACACCAAAACAAAACC
*
1756 CAAAAAAACCACCAAAACAA
1 CAACAAAA-CACCAAAACAA
1776 GGGGGGGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.27
21 8 0.24
22 7 0.21
23 1 0.03
24 8 0.24
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (23 bp):
CAACAAAACACCAAAACAAAACC
Found at i:1741 original size:14 final size:14
Alignment explanation
Indices: 1708--1760 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
1698 AAAAAACACC
1708 ACCAAC-AA-CAAA
1 ACCAACAAACCAAA
*
1720 A-CACCAAACCAAA
1 ACCAACAAACCAAA
1733 ACCAACAAACCAAA
1 ACCAACAAACCAAA
* *
1747 AACAA-AACCCAAA
1 ACCAACAAACCAAA
1760 A
1 A
1761 AAACCACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 3 0.09
12 3 0.09
13 13 0.38
14 15 0.44
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (14 bp):
ACCAACAAACCAAA
Found at i:1745 original size:33 final size:30
Alignment explanation
Indices: 1708--1771 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 30
1698 AAAAAACACC
*
1708 ACCAACAACAAAACACCAAACCAAAACCAACAA
1 ACCAAAAACAAAAC-CCAAA--AAAACCAACAA
*
1741 ACCAAAAACAAAACCCAAAAAAACCACCAA
1 ACCAAAAACAAAACCCAAAAAAACCAACAA
1771 A
1 A
1772 ACAAGGGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.38
32 5 0.17
33 13 0.45
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (30 bp):
ACCAAAAACAAAACCCAAAAAAACCAACAA
Found at i:1804 original size:10 final size:9
Alignment explanation
Indices: 1776--1813 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1766 ACCAAAACAA
1776 GGGGGG-GG
1 GGGGGGTGG
1784 GGGGGGTGG
1 GGGGGGTGG
1793 GGGGGGTCGG
1 GGGGGGT-GG
*
1803 GGCGGGTGG
1 GGGGGGTGG
1812 GG
1 GG
1814 TCGGTGGGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 6 0.22
9 13 0.48
10 8 0.30
ACGTcount: A:0.00, C:0.05, G:0.87, T:0.08
Consensus pattern (9 bp):
GGGGGGTGG
Found at i:1804 original size:15 final size:15
Alignment explanation
Indices: 1776--1832 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1766 ACCAAAACAA
** *
1776 GGGGGGGGGGGGGGT
1 GGGGGGGGTCGGGGC
1791 GGGGGGGGTCGGGGC
1 GGGGGGGGTCGGGGC
*
1806 GGGTGGGGTCGGTGGGC
1 GGGGGGGGTC-G-GGGC
1823 GTGGGGGGGT
1 G-GGGGGGGT
1833 GTTTTGTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 21 0.62
16 1 0.03
17 5 0.15
18 7 0.21
ACGTcount: A:0.00, C:0.07, G:0.81, T:0.12
Consensus pattern (15 bp):
GGGGGGGGTCGGGGC
Found at i:1958 original size:1 final size:1
Alignment explanation
Indices: 1954--2027 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
1944 GGGGTGTGGT
* * * * * * * * * *
1954 GGGGGGGGGTGGGGTGGGGGGTGGGGGGGTGGGGGGGGGGGGGGTGGGTGGGGTGGGGGTGGTGT
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2019 GGGGGGGGG
1 GGGGGGGGG
2028 TGGTGGGAAC
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (1 bp):
G
Found at i:1972 original size:35 final size:32
Alignment explanation
Indices: 1929--2030 Score: 118
Period size: 35 Copynumber: 3.1 Consensus size: 32
1919 ATTCTTGGTG
1929 GGGGTGGGGGGTTTTGGGGTGTGGTGGGGGGGGGT
1 GGGGTGGGGGG--TTGGGGTG-GGTGGGGGGGGGT
*
1964 GGGGTGGGGGG-TGGGG-GGGTGGGGGGGGGG
1 GGGGTGGGGGGTTGGGGTGGGTGGGGGGGGGT
*
1994 GGGGTGGGTGGGGTGGGGGTGGTGTGGGGGGGGGT
1 GGGGT-GG-GGGGTTGGGGTGG-GTGGGGGGGGGT
2029 GG
1 GG
2031 TGGGAACAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
30 17 0.29
31 3 0.05
32 9 0.15
33 4 0.07
34 2 0.03
35 24 0.41
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (32 bp):
GGGGTGGGGGGTTGGGGTGGGTGGGGGGGGGT
Found at i:1985 original size:30 final size:30
Alignment explanation
Indices: 1928--2034 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 30
1918 AATTCTTGGT
1928 GGGGGTGGGGGGTTTTGGGGTGTGGTGGGGGGGG
1 GGGGGTGGGGGG---TGGGG-GTGGTGGGGGGGG
1962 GTGGGGTGGGGGGTGGGGG-GGTGGGGGGGGG
1 G-GGGGTGGGGGGTGGGGGTGGT-GGGGGGGG
1993 GGGGGTGGGTGGGGTGGGGGTGGTGTGGGGGGG
1 GGGGGT-GG-GGGGTGGGGGTGGTG-GGGGGGG
*
2026 GGTGGTGGG
1 GGGGGTGGG
2035 AACAAAACCA
Statistics
Matches: 66, Mismatches: 1, Indels: 15
0.80 0.01 0.18
Matches are distributed among these distances:
30 8 0.12
31 13 0.20
32 18 0.27
33 15 0.23
34 1 0.02
35 11 0.17
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (30 bp):
GGGGGTGGGGGGTGGGGGTGGTGGGGGGGG
Found at i:2023 original size:33 final size:31
Alignment explanation
Indices: 1928--2034 Score: 119
Period size: 33 Copynumber: 3.3 Consensus size: 31
1918 AATTCTTGGT
*
1928 GGGGGTGGGGGGTTTTGGGGTGTGGTGGGGGGGG
1 GGGGGTGGGGGG--GTGGGG-GTGGTGGGGGGGG
1962 GTGGGGT-GGGGGGTGGGGG-GGTGGGGGGGGG
1 G-GGGGTGGGGGGGTGGGGGTGGT-GGGGGGGG
1993 GGGGGTGGGTGGGGTGGGGGTGGTGTGGGGGGG
1 GGGGGTGGG-GGGGTGGGGGTGGTG-GGGGGGG
*
2026 GGTGGTGGG
1 GGGGGTGGG
2035 AACAAAACCA
Statistics
Matches: 65, Mismatches: 2, Indels: 13
0.81 0.03 0.16
Matches are distributed among these distances:
30 8 0.12
31 12 0.18
32 16 0.25
33 18 0.28
34 6 0.09
35 5 0.08
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (31 bp):
GGGGGTGGGGGGGTGGGGGTGGTGGGGGGGG
Found at i:2032 original size:15 final size:14
Alignment explanation
Indices: 1951--2030 Score: 97
Period size: 15 Copynumber: 5.4 Consensus size: 14
1941 TTTGGGGTGT
1951 GGTGGGGGGGGGTGG
1 GGTGGGGGGGGG-GG
1966 GGTGGGGGGTGGGGG
1 GGTGGGGGG-GGGGG
1981 GGTGGGGGGGGGGGG
1 GGT-GGGGGGGGGGG
*
1996 GGTGGGTGGGGTGGG
1 GGTGGG-GGGGGGGG
*
2011 GGTGGTGTGGGGGGG
1 GGTGG-GGGGGGGGG
2026 GGTGG
1 GGTGG
2031 TGGGAACAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.05
15 45 0.78
16 10 0.17
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (14 bp):
GGTGGGGGGGGGGG
Found at i:2097 original size:32 final size:33
Alignment explanation
Indices: 2041--2119 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
2031 TGGGAACAAA
* ** *
2041 ACCACCCAACCCACCCCACCCCCAAACCAACAC
1 ACCACACAACCCACCAAACACCCAAACCAACAC
* *
2074 A-CACACAACCCACCAAACACCCAAACCACCCC
1 ACCACACAACCCACCAAACACCCAAACCAACAC
*
2106 ACCACACCACCCAC
1 ACCACACAACCCAC
2120 ACCTCAAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 26 0.68
33 12 0.32
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (33 bp):
ACCACACAACCCACCAAACACCCAAACCAACAC
Found at i:2102 original size:16 final size:16
Alignment explanation
Indices: 2061--2103 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2051 CCACCCCACC
* *
2061 CCCAAACCAACACACA
1 CCCAAACCACCAAACA
* *
2077 CACAACCCACCAAACA
1 CCCAAACCACCAAACA
2093 CCCAAACCACC
1 CCCAAACCACC
2104 CCACCACACC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (16 bp):
CCCAAACCACCAAACA
Found at i:2198 original size:18 final size:18
Alignment explanation
Indices: 2177--2274 Score: 53
Period size: 17 Copynumber: 5.5 Consensus size: 18
2167 CCCACAAACA
2177 CACCCCCACACCCCCACC
1 CACCCCCACACCCCCACC
* * **
2195 CACCCACAAAAAACCCACC
1 CACCC-CCACACCCCCACC
* *
2214 C-CCACCAAACACCCCACCC
1 CACCCCCACAC-CCCCA-CC
* *
2233 CCCCCCCCCACCCCC-CC
1 CACCCCCACACCCCCACC
2250 CACCCCC-CAACCCCC-CC
1 CACCCCCAC-ACCCCCACC
2267 C-CCCCCAC
1 CACCCCCAC
2275 CCTCCAAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
16 6 0.10
17 22 0.35
18 11 0.18
19 17 0.27
20 6 0.10
ACGTcount: A:0.24, C:0.76, G:0.00, T:0.00
Consensus pattern (18 bp):
CACCCCCACACCCCCACC
Found at i:2234 original size:1 final size:1
Alignment explanation
Indices: 2225--2272 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
2215 CCACCAAACA
* * * **
2225 CCCCACCCCCCCCCCCCACCCCCCCCACCCCCCAACCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2273 ACCCTCCAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.10, C:0.90, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2237 original size:22 final size:22
Alignment explanation
Indices: 2207--2257 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2197 CCCACAAAAA
*
2207 ACCCACCCCCACCAAACACCCC
1 ACCCCCCCCCACCAAACACCCC
* ** *
2229 ACCCCCCCCCCCCACCCCCCCC
1 ACCCCCCCCCACCAAACACCCC
2251 ACCCCCC
1 ACCCCCC
2258 AACCCCCCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (22 bp):
ACCCCCCCCCACCAAACACCCC
Found at i:2246 original size:31 final size:31
Alignment explanation
Indices: 2208--2276 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
2198 CCACAAAAAA
2208 CCCACCCCCACCAAACACCCC-A-CCCCCCCCC
1 CCCACCCCC-CC-AACACCCCAACCCCCCCCCC
* *
2239 CCCACCCCCCCCACCCCCCAACCCCCCCCCC
1 CCCACCCCCCCAACACCCCAACCCCCCCCCC
2270 CCCACCC
1 CCCACCC
2277 TCCAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 6 0.18
30 3 0.09
31 25 0.74
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (31 bp):
CCCACCCCCCCAACACCCCAACCCCCCCCCC
Found at i:2263 original size:22 final size:22
Alignment explanation
Indices: 2225--2281 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2215 CCACCAAACA
**
2225 CCCCACCCCCCCCCCCCACCCC
1 CCCCACCCCCCAACCCCACCCC
*
2247 CCCCACCCCCCAACCCCCCCCC
1 CCCCACCCCCCAACCCCACCCC
*
2269 CCCCACCCTCCAA
1 CCCCACCCCCCAA
2282 AAAACAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.14, C:0.84, G:0.00, T:0.02
Consensus pattern (22 bp):
CCCCACCCCCCAACCCCACCCC
Found at i:2305 original size:15 final size:14
Alignment explanation
Indices: 2279--2436 Score: 120
Period size: 14 Copynumber: 10.7 Consensus size: 14
2269 CCCCACCCTC
2279 CAAAAAACAAAAAACCA
1 CAAAAAA-AAAAAA--A
2296 CAAAAAAAAAAAAAA
1 C-AAAAAAAAAAAAA
**
2311 CAAAAAAACCAAAA
1 CAAAAAAAAAAAAA
2325 CAAAAAAAAAAAAAA
1 C-AAAAAAAAAAAAA
2340 CAAAAAAACAAAAAA
1 CAAAAAAA-AAAAAA
2355 C-AAAAAAAAAAAA
1 CAAAAAAAAAAAAA
****
2368 CAAAAAAAAACCCC
1 CAAAAAAAAAAAAA
* * *
2382 CTCACAACAAAAAAA
1 C-AAAAAAAAAAAAA
* *
2397 CAAAAAAAACACAA
1 CAAAAAAAAAAAAA
*
2411 CAAACAAAAACCAAAA
1 CAAA-AAAAA-AAAAA
2427 CAAAAAAAAA
1 CAAAAAAAAA
2437 CCAAAAAAAC
Statistics
Matches: 112, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
13 7 0.06
14 46 0.41
15 38 0.34
16 8 0.07
17 7 0.06
18 6 0.05
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.01
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:2333 original size:30 final size:30
Alignment explanation
Indices: 2297--2455 Score: 144
Period size: 31 Copynumber: 5.1 Consensus size: 30
2287 AAAAAACCAC
2297 AAAAAAAAAAAAAACAAAAAAACCAAAAC-
1 AAAAAAAAAAAAAACAAAAAAACCAAAACA
*
2326 AAAAAAAAAAAAAACAAAAAAACAAAAAACA
1 AAAAAAAAAAAAAACAAAAAAAC-CAAAACA
* *
2357 AAAAAAAAAAACAAA-AAAAAACCCCCTCACAACA
1 AAAAAAAAAAA-AAACAAAAAA---AC-CAAAACA
* *
2391 AAAAAACAAAAAAAACACAACAAACAAAAACCA
1 AAAAAA-AAAAAAAACA-AAAAAACCAAAA-CA
* *
2424 AAACAAAAAAAAACCAAAAAAA-CACAAACA
1 AAAAAAAAAAAAAACAAAAAAACCA-AAACA
2454 AA
1 AA
2456 CTAAAAACCA
Statistics
Matches: 106, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
29 23 0.22
30 10 0.09
31 25 0.24
32 15 0.14
33 8 0.08
34 15 0.14
35 6 0.06
36 4 0.04
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.01
Consensus pattern (30 bp):
AAAAAAAAAAAAAACAAAAAAACCAAAACA
Found at i:2337 original size:29 final size:29
Alignment explanation
Indices: 2280--2375 Score: 141
Period size: 28 Copynumber: 3.5 Consensus size: 29
2270 CCCACCCTCC
2280 AAAAAAC-AAAAAACC---ACAAAAAAAA
1 AAAAAACAAAAAAACCAAAACAAAAAAAA
2305 AAAAAACAAAAAAACCAAAACAAAAAAAA
1 AAAAAACAAAAAAACCAAAACAAAAAAAA
2334 AAAAAACAAAAAAA-CAAAA-AACAAAAAA
1 AAAAAACAAAAAAACCAAAACAA-AAAAAA
2362 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
2376 AACCCCCTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
25 7 0.11
26 8 0.12
27 2 0.03
28 25 0.38
29 24 0.36
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (29 bp):
AAAAAACAAAAAAACCAAAACAAAAAAAA
Found at i:2376 original size:29 final size:29
Alignment explanation
Indices: 2295--2435 Score: 135
Period size: 29 Copynumber: 4.9 Consensus size: 29
2285 ACAAAAAACC
*
2295 ACAAAAAAAAAAAAAACAAAAAAACCAAA
1 ACAAAAAAAAAAAAAACAAAAAAAACAAA
2324 ACAAAAAAAAAAAAAAC-AAAAAAACAAA
1 ACAAAAAAAAAAAAAACAAAAAAAACAAA
**
2352 A-AACAAAAAAAAAAAACAAAAAAAA-ACCC
1 ACAA-AAAAAAAAAAAACAAAAAAAACA-AA
* ** * * *
2381 CCTCACAACAAAAAAACAAAAAAAACACA
1 ACAAAAAAAAAAAAAACAAAAAAAACAAA
**
2410 ACAAACAAAAACCAAAACAAAAAAAA
1 ACAAA-AAAAAAAAAAACAAAAAAAA
2436 ACCAAAAAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
27 2 0.02
28 25 0.28
29 46 0.51
30 17 0.19
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.01
Consensus pattern (29 bp):
ACAAAAAAAAAAAAAACAAAAAAAACAAA
Found at i:2394 original size:59 final size:59
Alignment explanation
Indices: 2280--2442 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 59
2270 CCCACCCTCC
*
2280 AAAAAACAAAAAACCACAAAAAAAAAAAAAACAAAAAAACCAAAACAAAAAAAAAAAA-AACA
1 AAAAAACAAAAAA-CA-AAAAAAAAAAACAA-AAAAAAACCAAAACAAAAAAAAAAAACAA-A
**** * *
2342 AAAAAACAAAAAACAAAAAAAAAAAACAAAAAAAAACCCCCTCACAACAAAAAAACAAA
1 AAAAAACAAAAAACAAAAAAAAAAAACAAAAAAAAACCAAAACAAAAAAAAAAAACAAA
* **
2401 AAAAACACAACAAAC-AAAAACCAAAACAAAAAAAAACCAAAA
1 AAAAA-ACAAAAAACAAAAAAAAAAAACAAAAAAAAACCAAAA
2443 AAACACAAAC
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 47 0.55
60 23 0.27
61 2 0.02
62 13 0.15
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.01
Consensus pattern (59 bp):
AAAAAACAAAAAACAAAAAAAAAAAACAAAAAAAAACCAAAACAAAAAAAAAAAACAAA
Found at i:2396 original size:1 final size:1
Alignment explanation
Indices: 2297--2377 Score: 90
Period size: 1 Copynumber: 81.0 Consensus size: 1
2287 AAAAAACCAC
* ** * * * *
2297 AAAAAAAAAAAAAACAAAAAAACCAAAACAAAAAAAAAAAAAACAAAAAAACAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
2362 AAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAA
2378 CCCCCTCACA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2410 original size:19 final size:19
Alignment explanation
Indices: 2388--2462 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
2378 CCCCCTCACA
2388 ACAAAAAAACAAAAAAAAC
1 ACAAAAAAACAAAAAAAAC
*
2407 ACAACAAACAA-AAACCAAAAC
1 ACAA-AAA-AACAAA-AAAAAC
* *
2428 AAAAAAAAACCAAAAAAAC
1 ACAAAAAAACAAAAAAAAC
*
2447 ACAAACAAACTAAAAA
1 ACAAAAAAAC-AAAAA
2463 CCACCCCCCC
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 19 0.43
20 15 0.34
21 10 0.23
ACGTcount: A:0.79, C:0.20, G:0.00, T:0.01
Consensus pattern (19 bp):
ACAAAAAAACAAAAAAAAC
Found at i:2428 original size:16 final size:16
Alignment explanation
Indices: 2393--2452 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
2383 TCACAACAAA
2393 AAAACAAA-AAAAA-C
1 AAAACAAACAAAAACC
*
2407 ACAACAAACAAAAACC
1 AAAACAAACAAAAACC
*
2423 AAAACAAAAAAAAACC
1 AAAACAAACAAAAACC
*
2439 AAAA-AAACACAAAC
1 AAAACAAACAAAAAC
2453 AAACTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
14 7 0.18
15 13 0.33
16 19 0.49
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAACAAAAACC
Found at i:2451 original size:59 final size:56
Alignment explanation
Indices: 2280--2462 Score: 146
Period size: 59 Copynumber: 3.2 Consensus size: 56
2270 CCCACCCTCC
* *
2280 AAAAAAC-AAAAAACCACAAAAA-AAAAAAAAAC--AAAAAAACCAAAACAAA-AAA
1 AAAAAACAAAAAAAACACAAAAACAAAAAAAAACAAAAAAAAACCAAAA-AAACACA
* *****
2332 AAAAAAAACAAAAAAACA-AAAAACAAAAAAAAAAAACAAAAAAAAACC-CCCTCACAACA
1 AAAAAACA-AAAAAAACACAAAAAC---AAAAAAAAACAAAAAAAAACCAAAAAAAC-ACA
2391 AAAAAACAAAAAAAACACAACAAACAAAAACCAAAACAAAAAAAAACCAAAAAAACACA
1 AAAAAACAAAAAAAACACAA-AAACAAAAA--AAAACAAAAAAAAACCAAAAAAACACA
* *
2450 AACAAACTAAAAA
1 AAAAAACAAAAAA
2463 CCACCCCCCC
Statistics
Matches: 100, Mismatches: 16, Indels: 23
0.72 0.12 0.17
Matches are distributed among these distances:
52 6 0.06
53 5 0.05
54 8 0.08
57 16 0.16
58 9 0.09
59 50 0.50
60 6 0.06
ACGTcount: A:0.80, C:0.19, G:0.00, T:0.01
Consensus pattern (56 bp):
AAAAAACAAAAAAAACACAAAAACAAAAAAAAACAAAAAAAAACCAAAAAAACACA
Found at i:2456 original size:10 final size:10
Alignment explanation
Indices: 2287--2456 Score: 83
Period size: 9 Copynumber: 17.7 Consensus size: 10
2277 TCCAAAAAAC
2287 AAAAAAC-CA
1 AAAAAACACA
*
2296 CAAAAA-A-A
1 AAAAAACACA
2304 AAAAAA-ACA
1 AAAAAACACA
2313 AAAAAAC-CA
1 AAAAAACACA
*
2322 AAACAAA-AAA
1 AAA-AAACACA
*
2332 AAAAAAAACA
1 AAAAAACACA
2342 AAAAAACA-A
1 AAAAAACACA
* *
2351 AAAACAAAAAA
1 AAAA-AACACA
*
2362 AAAAAACAAA
1 AAAAAACACA
* *
2372 AAAAAACCCC
1 AAAAAACACA
*** *
2382 CTCACA-ACA
1 AAAAAACACA
2391 AAAAAACA-A
1 AAAAAACACA
2400 AAAAAACAC-
1 AAAAAACACA
* *
2409 AACAAACAAA
1 AAAAAACACA
*
2419 AACCAAAACAAA
1 AA--AAAACACA
2431 AAAAAAC-CA
1 AAAAAACACA
2440 AAAAAACACA
1 AAAAAACACA
*
2450 AACAAAC
1 AAAAAAC
2457 TAAAAACCAC
Statistics
Matches: 122, Mismatches: 25, Indels: 27
0.70 0.14 0.16
Matches are distributed among these distances:
8 7 0.06
9 52 0.43
10 49 0.40
11 5 0.04
12 9 0.07
ACGTcount: A:0.80, C:0.19, G:0.00, T:0.01
Consensus pattern (10 bp):
AAAAAACACA
Found at i:2456 original size:29 final size:28
Alignment explanation
Indices: 2281--2462 Score: 124
Period size: 29 Copynumber: 6.4 Consensus size: 28
2271 CCACCCTCCA
*
2281 AAAAACAAAAAACCAC-AA-AAA-AAAA
1 AAAAACAAAAAAACACAAACAAACAAAA
*
2306 AAAAACAAAAAAAC-CAAAACAAAAAAAAA
1 AAAAACAAAAAAACAC-AAAC-AAACAAAA
*
2335 AAAAACAAAAAAACAAAAAACAAA-AAAA
1 AAAAACAAAAAAAC-ACAAACAAACAAAA
* *** **
2363 AAAAACAAAAAAAAACCCCCTCACAACAA
1 AAAAACAAAAAAACACAAACAAACAA-AA
2392 AAAAACAAAAAAA-ACACAACAAACAAAA
1 AAAAACAAAAAAACACA-AACAAACAAAA
* * *
2420 ACCAAAACAAAAAAAAACCAAAAAAACACAA
1 A--AAAACAAAAAAACA-CAAACAAACAAAA
* *
2451 ACAAACTAAAAA
1 AAAAACAAAAAA
2463 CCACCCCCCC
Statistics
Matches: 125, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
24 1 0.01
25 13 0.10
26 2 0.02
27 3 0.02
28 27 0.22
29 50 0.40
30 16 0.13
31 11 0.09
32 2 0.02
ACGTcount: A:0.80, C:0.19, G:0.00, T:0.01
Consensus pattern (28 bp):
AAAAACAAAAAAACACAAACAAACAAAA
Found at i:2461 original size:26 final size:24
Alignment explanation
Indices: 2280--2465 Score: 111
Period size: 23 Copynumber: 7.4 Consensus size: 24
2270 CCCACCCTCC
2280 AAAAAA-CAAAAAACCACAAAA-AAA
1 AAAAAACCAAAAAA--ACAAAACAAA
*
2304 AAAAAAACAAAAAAACCAAAAC--A
1 AAAAAACCAAAAAAA-CAAAACAAA
2327 AAAAAA--AAAAAAACAAAA-AAA
1 AAAAAACCAAAAAAACAAAACAAA
*
2348 CAAAAAA-CAAAAAAAAAAAACAAA
1 -AAAAAACCAAAAAAACAAAACAAA
*
2372 AAAAAACCCCCTCACAACAAA-AAAACAAA
1 AAAAAA----C-CA-AAAAAACAAAACAAA
2401 AAAAACACAACAAACAAAAACCAAAACAAA
1 AAAAA-AC--C-AA-AAAAA-CAAAACAAA
2431 AAAAAACCAAAAAAACACAAACAAA
1 AAAAAACCAAAAAAACA-AAACAAA
*
2456 CTAAAAACCA
1 -AAAAAACCA
2466 CCCCCCCCAC
Statistics
Matches: 134, Mismatches: 5, Indels: 44
0.73 0.03 0.24
Matches are distributed among these distances:
20 5 0.04
21 8 0.06
22 6 0.04
23 25 0.19
24 16 0.12
25 19 0.14
26 11 0.08
27 3 0.02
28 5 0.04
29 17 0.13
30 19 0.14
ACGTcount: A:0.80, C:0.19, G:0.00, T:0.01
Consensus pattern (24 bp):
AAAAAACCAAAAAAACAAAACAAA
Found at i:2517 original size:36 final size:33
Alignment explanation
Indices: 2469--2549 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 33
2459 AAAACCACCC
*
2469 CCCCCACACACCCCCCCCACCACCCCCAACACCAA
1 CCCCCACCCACCCCCCCCACC-CCCCC-ACACCAA
*
2504 CCCACCACCCACCCCCCCCCACCCCCCCACACCCA
1 CCC-CCACCCA-CCCCCCCCACCCCCCCACACCAA
2539 CCCCC-CCCACC
1 CCCCCACCCACC
2550 ACCACAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.05
33 4 0.10
34 2 0.05
35 12 0.29
36 11 0.26
37 11 0.26
ACGTcount: A:0.22, C:0.78, G:0.00, T:0.00
Consensus pattern (33 bp):
CCCCCACCCACCCCCCCCACCCCCCCACACCAA
Found at i:2527 original size:14 final size:14
Alignment explanation
Indices: 2504--2546 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2494 CCAACACCAA
2504 CCCA-CCACCCACCC
1 CCCACCCACCC-CCC
2518 CCC-CCCACCCCCC
1 CCCACCCACCCCCC
*
2531 CACACCCACCCCCC
1 CCCACCCACCCCCC
2545 CC
1 CC
2547 ACCACCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.16, C:0.84, G:0.00, T:0.00
Consensus pattern (14 bp):
CCCACCCACCCCCC
Found at i:2542 original size:60 final size:59
Alignment explanation
Indices: 2463--2584 Score: 167
Period size: 60 Copynumber: 2.1 Consensus size: 59
2453 AAACTAAAAA
* * *
2463 CCACCCCCCCCACACACCCCCCCCACCACCCCCAACACC-A-ACCCACCACCCACCCCCCC
1 CCACCCCCCCCACACACCCCCCCCACCACCACAAAC-CCAACACCCACC-CCCACACCCCC
*
2522 CCACCCCCCCACACCCACCCCCCCCACCACCACAAACCCAACACCCACCCCCACACCCCC
1 CCACCCCCCC-CACACACCCCCCCCACCACCACAAACCCAACACCCACCCCCACACCCCC
2582 CCA
1 CCA
2585 ACAACCACCC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 12 0.21
60 37 0.66
61 7 0.12
ACGTcount: A:0.25, C:0.75, G:0.00, T:0.00
Consensus pattern (59 bp):
CCACCCCCCCCACACACCCCCCCCACCACCACAAACCCAACACCCACCCCCACACCCCC
Found at i:2546 original size:23 final size:23
Alignment explanation
Indices: 2464--2618 Score: 79
Period size: 23 Copynumber: 6.6 Consensus size: 23
2454 AACTAAAAAC
*
2464 CACCC-CCCCCACACACCCCCCC-
1 CACCCACCCCC-CCCACCCCCCCA
** **
2486 CA-CCACCCCCAACACCAACCCA
1 CACCCACCCCCCCCACCCCCCCA
2508 CCACCCACCCCCCCCCACCCCCCCA
1 -CACCCA-CCCCCCCCACCCCCCCA
* *
2533 CACCCACCCCCCCCACCACCACA
1 CACCCACCCCCCCCACCCCCCCA
*
2556 AACCCAACACCCACCCCCACACCCCCC-
1 CA-CC--CACCC-CCCCCAC-CCCCCCA
* * * *
2583 CAACAACCACCCACCA-CCCCCAA
1 CACCCACC-CCCCCCACCCCCCCA
2606 CACCC-CCCCCCCC
1 CACCCACCCCCCCC
2619 TTTTTTTTTT
Statistics
Matches: 101, Mismatches: 20, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
21 15 0.15
22 14 0.14
23 21 0.21
24 19 0.19
25 14 0.14
26 6 0.06
27 8 0.08
28 4 0.04
ACGTcount: A:0.26, C:0.74, G:0.00, T:0.00
Consensus pattern (23 bp):
CACCCACCCCCCCCACCCCCCCA
Found at i:2552 original size:36 final size:38
Alignment explanation
Indices: 2463--2618 Score: 116
Period size: 37 Copynumber: 4.3 Consensus size: 38
2453 AAACTAAAAA
2463 CCACCCCCCCCA-CACACCCCCCCCACCACCCCCAACAC
1 CCACCCCCCCCACCAC-CCCCCCCCACCACCCCCAACAC
* * *
2501 CAACCCACCAC-CCACCCCCCCCCACC-CCCCC-ACAC
1 CCACCCCCCCCACCACCCCCCCCCACCACCCCCAACAC
*** * *
2536 CCACCCCCCCCACCACCACAAACCCA--ACACCC-ACCC
1 CCACCCCCCCCACCACC-CCCCCCCACCACCCCCAACAC
** *
2572 CCACACCCCCCCA--ACAACCACCCACCACCCCCAACAC
1 CCAC-CCCCCCCACCACCCCCCCCCACCACCCCCAACAC
2609 CC-CCCCCCCC
1 CCACCCCCCCC
2619 TTTTTTTTTT
Statistics
Matches: 93, Mismatches: 17, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
34 5 0.05
35 21 0.23
36 27 0.29
37 29 0.31
38 11 0.12
ACGTcount: A:0.26, C:0.74, G:0.00, T:0.00
Consensus pattern (38 bp):
CCACCCCCCCCACCACCCCCCCCCACCACCCCCAACAC
Found at i:2600 original size:60 final size:58
Alignment explanation
Indices: 2471--2603 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 58
2461 AACCACCCCC
* * * * *
2471 CCCACACACCCCCCCCACCACCCCCAACACCAACCCACCACCCACCCCCCCCCACCCCC
1 CCCAC-CACCCCCCCCACCACCACAAACACCAACCCACCACCCACCCCCCCCAACACCA
2530 CCACACCCACCCCCCCCACCACCACAAAC-CCAACACCCACC-CCCACACCCCCCCAACAACCA
1 CC-CA-CCACCCCCCCCACCACCACAAACACC-A-ACCCACCACCCAC-CCCCCCCAAC-ACCA
2592 CCCACCACCCCC
1 CCCACCACCCCC
2604 AACACCCCCC
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
59 4 0.06
60 36 0.57
61 19 0.30
62 4 0.06
ACGTcount: A:0.27, C:0.73, G:0.00, T:0.00
Consensus pattern (58 bp):
CCCACCACCCCCCCCACCACCACAAACACCAACCCACCACCCACCCCCCCCAACACCA
Found at i:2623 original size:1 final size:1
Alignment explanation
Indices: 2619--2656 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
2609 CCCCCCCCCC
2619 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2657 AACAAAACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2754 original size:5 final size:5
Alignment explanation
Indices: 2753--2990 Score: 112
Period size: 5 Copynumber: 45.4 Consensus size: 5
2743 GGGGGGGTGG
* * *
2753 GGGGT GGTGT GTGGT GGGGGT GTGGT GGTGGGT GGGGTT GGGGGT GGGGTT
1 GGGGT GGGGT GGGGT -GGGGT GGGGT -G-GGGT GGGG-T -GGGGT GGGG-T
* *
2804 GGGG- GGGGTT GGTGT GGGGT GGGGT GGGGGT GGGTGTT TGGGT GGGGGT
1 GGGGT GGGG-T GGGGT GGGGT GGGGT -GGGGT GGG-G-T GGGGT -GGGGT
* * * *
2853 GGGGT GGGG- GGGGG GGGTGT GGGGG GGGGT GGGTT GGGGG GGGGT GGGG-
1 GGGGT GGGGT GGGGT GGG-GT GGGGT GGGGT GGGGT GGGGT GGGGT GGGGT
* * ** *
2902 GGGGTT GGGG- GTGGG- GGGGT GGGGG GGTGGT GGTGT GTTTGT GGTGT
1 GGGG-T GGGGT G-GGGT GGGGT GGGGT GG-GGT GGGGT G-GGGT GGGGT
* * *
2949 GGTGT GGTGG- GGGGT GGTGT GGGGT GGTGGT -GGTT GGGGT GG
1 GGGGT GG-GGT GGGGT GGGGT GGGGT GG-GGT GGGGT GGGGT GG
2991 TTGGTTGGTT
Statistics
Matches: 182, Mismatches: 27, Indels: 48
0.71 0.11 0.19
Matches are distributed among these distances:
4 20 0.11
5 105 0.58
6 47 0.26
7 10 0.05
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (5 bp):
GGGGT
Found at i:2765 original size:25 final size:25
Alignment explanation
Indices: 2737--3097 Score: 103
Period size: 27 Copynumber: 14.1 Consensus size: 25
2727 AAAATGGGTT
2737 TGTGGGGGGGGGGTGGGGGGTGGTG
1 TGTGGGGGGGGGGTGGGGGGTGGTG
* *
2762 TGTGGTGGGGGTGTGGTGGTGGGTGGGG
1 TGTGG-GGGGG-G-GGTGGGGGGTGGTG
*
2790 T-TGGGGGTGGGGTTGGGGGG-GGTTGG
1 TGTGGGGG-GGGGGTGGGGGGTGG-T-G
*
2816 TGTGGGGTGGGGTGG-GGGTGGGTGTTTG
1 TGTGGGG-GGGG-GGTGGG-GGGTG-GTG
* * *
2844 GGTGGGGGTGGGGTGGGGGG-GGGG
1 TGTGGGGGGGGGGTGGGGGGTGGTG
*
2868 GGTGTGGGGGGGGGTGGGTTGGG-GG-G
1 TGTG-GGGGGGGGGTGGG--GGGTGGTG
*
2894 -G-GGTGGGGGGGGTTGGGGGTGG-G
1 TGTGG-GGGGGGGGTGGGGGGTGGTG
* *
2917 -G-GGGTGGGGGGGT-GGTGGTGTGTT
1 TGTGGG-GGGGGGGTGGGGGGTG-GTG
* *
2941 TGTGGTGTGGTGTGGTGGGGGGTGGTG
1 TGTGG-G-GGGGGGGTGGGGGGTGGTG
*
2968 TG-GGGTGGTGGTGGTTGGGGTGGTTGGT-
1 TGTGGG-GG-GG-GGGTGGGG-GG-TGGTG
** ** * *
2996 TG-GTTTGGGGGTTTGGGTGTTGG-G
1 TGTG-GGGGGGGGGTGGGGGGTGGTG
* * * *
3020 TTTTGGGGGGTGGTGGGG-GTGGGG
1 TGTGGGGGGGGGGTGGGGGGTGGTG
*
3044 GGTGGGGGGGGTGGTGGGGGGGTGG-G
1 TGTGGGGGGGG-GGT-GGGGGGTGGTG
*
3070 -GTGGGGGGGTGTGGTGGGGGGGGGTG
1 TGTGGGGGGG-G-GGTGGGGGGTGGTG
3096 TG
1 TG
3098 GTTGGTGGTG
Statistics
Matches: 256, Mismatches: 41, Indels: 76
0.69 0.11 0.20
Matches are distributed among these distances:
22 10 0.04
23 19 0.07
24 39 0.15
25 52 0.20
26 39 0.15
27 53 0.21
28 38 0.15
29 6 0.02
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (25 bp):
TGTGGGGGGGGGGTGGGGGGTGGTG
Found at i:2797 original size:12 final size:11
Alignment explanation
Indices: 2738--2936 Score: 155
Period size: 11 Copynumber: 18.3 Consensus size: 11
2728 AAATGGGTTT
*
2738 GTGGGGGGGGG
1 GTGGGGTGGGG
2749 GTGGGG-GGTGG
1 GTGGGGTGG-GG
*
2760 TGTGTGGTGGGG
1 -GTGGGGTGGGG
*
2772 GTGTGGTGGTGG
1 GTGGGGTGG-GG
2784 GTGGGGTTGGGG
1 GTGGGG-TGGGG
*
2796 GTGGGGTTGGG
1 GTGGGGTGGGG
* *
2807 G-GGGGTTGGT
1 GTGGGGTGGGG
2817 GTGGGGT-GGG
1 GTGGGGTGGGG
2827 GTGGGGGTGGGTG
1 GT-GGGGTGGG-G
* *
2840 TTTGGGTGGGG
1 GTGGGGTGGGG
2851 GTGGGGTGGGG
1 GTGGGGTGGGG
*
2862 G-GGGG-GGGT
1 GTGGGGTGGGG
2871 GTGGGG-GGGG
1 GTGGGGTGGGG
*
2881 GTGGGTTGGGG
1 GTGGGGTGGGG
2892 G-GGGGTGGGG
1 GTGGGGTGGGG
*
2902 G-GGGTTGGGG
1 GTGGGGTGGGG
2912 GTGGGG-GGGTG
1 GTGGGGTGGG-G
* *
2923 GGGGGGTGGTG
1 GTGGGGTGGGG
2934 GTG
1 GTG
2937 TGTTTGTGGT
Statistics
Matches: 156, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
9 4 0.03
10 52 0.33
11 60 0.38
12 33 0.21
13 7 0.04
ACGTcount: A:0.00, C:0.00, G:0.78, T:0.22
Consensus pattern (11 bp):
GTGGGGTGGGG
Found at i:2851 original size:1 final size:1
Alignment explanation
Indices: 2847--2928 Score: 56
Period size: 1 Copynumber: 82.0 Consensus size: 1
2837 GTGTTTGGGT
* * * * * ** * **
2847 GGGGGTGGGGTGGGGGGGGGGGGTGTGGGGGGGGGTGGGTTGGGGGGGGGTGGGGGGGGTTGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
* *
2912 GTGGGGGGGTGGGGGGG
1 GGGGGGGGGGGGGGGGG
2929 TGGTGGTGTG
Statistics
Matches: 61, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (1 bp):
G
Found at i:3006 original size:44 final size:42
Alignment explanation
Indices: 2915--3113 Score: 117
Period size: 44 Copynumber: 4.7 Consensus size: 42
2905 GTTGGGGGTG
*
2915 GGGGGGTGGGGGGGTGGTGGTGTGTTTGTGGTGTGGTGTGGT
1 GGGGGGTGGGGGGGTGGTGGTGTGTTGGTGGTGTGGTGTGGT
2957 GGGGGGTGGTGTGGGGTGGTGGTG-GTTGG-GGTGGTTGGT-TGGTT
1 GGGGGGTGG-G-GGGGTGGTGGTGTGTTGGTGGT-G-TGGTGTGG-T
* ** * * * *
3001 TGGGGGT--TTGGGTGTTGG-GTTTTGG-GGGGTGGTGGGGGT
1 GGGGGGTGGGGGGGTGGTGGTGTGTTGGTGGTGTGGT-GTGGT
* * * * *
3040 GGGGGGTGGGGGGGGTGGTGGGGGGGTGGGGTGGGGGGGTGTGGT
1 GGGGGGT-GGGGGGGTGGT-GGTGTGT-TGGTGGTGTGGTGTGGT
*
3085 GGGGGG-GGGTGTGGTTGGTGGTGTGTTGG
1 GGGGGGTGGG-G-GGGTGGTGGTGTGTTGG
3114 GTTTGGTGGG
Statistics
Matches: 119, Mismatches: 21, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
38 4 0.03
39 9 0.08
40 16 0.13
42 18 0.15
43 16 0.13
44 31 0.26
45 18 0.15
46 7 0.06
ACGTcount: A:0.00, C:0.00, G:0.70, T:0.30
Consensus pattern (42 bp):
GGGGGGTGGGGGGGTGGTGGTGTGTTGGTGGTGTGGTGTGGT
Found at i:3007 original size:19 final size:15
Alignment explanation
Indices: 2925--3005 Score: 64
Period size: 18 Copynumber: 5.3 Consensus size: 15
2915 GGGGGGTGGG
2925 GGGGTGGTGGTGTGTTT
1 GGGGTGGTGGTG-G-TT
2942 GTGGTGTGGT-GTGG-T
1 G-GG-GTGGTGGTGGTT
2957 GGGG-GGTGGT-G-T
1 GGGGTGGTGGTGGTT
2969 GGGGTGGTGGTGGTT
1 GGGGTGGTGGTGGTT
2984 GGGGTGGTTGGTTGGTTT
1 GGGGTGG-TGG-TGG-TT
3002 GGGG
1 GGGG
3006 GTTTGGGTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
12 9 0.16
13 9 0.16
14 3 0.05
15 10 0.18
16 3 0.05
17 5 0.09
18 11 0.20
19 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (15 bp):
GGGGTGGTGGTGGTT
Found at i:3007 original size:150 final size:147
Alignment explanation
Indices: 2740--3102 Score: 339
Period size: 150 Copynumber: 2.5 Consensus size: 147
2730 ATGGGTTTGT
* * * *
2740 GGGGGGGGGGTGGGGGGTGG-TGTGTGGTGGGGGTGTGGTGGTG-GGTGG-GGTTGGGGGTGGGG
1 GGGGGGGGGGTGGGGGG-GGTTG-GGGGTGGGGGGGTGGGGGGGTGGTGGTGGTTGGGGGTGGGG
*
2802 TTGGGGGGGGTTGGTGTGGGGTGGGGTGGGGGTGGGTGTTTGGGTGGGGGTGGGG-TGGGGGGGG
64 TTGGGGGGGGTTGGTGTGGGGTGGGGTGGGGGTGGGTGGTTGGGTGGGGGTGGGGTTGGGGGGGG
2866 GGGGTGTGGGGGGGGGTGG
129 GGGGTGTGGGGGGGGGTGG
* * *
2885 GTTGGGGGGGGGTGGGGGGGGTTGGGGGTGGGGGGGTGGGGGGGTGGTGGTGTGTTTGTGGTGTG
1 G--GGGGGGGGGTGGGGGGGGTTGGGGGTGGGGGGGTGGGGGGGTGGTGGTG-GTTGGGGGTGGG
** * ** *
2950 GTGTGGTGGGGGG-TGGTGTGGGGTGGTGGTGGTTG-GGGTGGTT-GGTTGGTTTGGGGGTTTGG
63 GT-TGG-GGGGGGTTGGTGTGGGGTGG-GGTGGGGGTGGGTGGTTGGGTGGGGGT-GGGGTTGGG
* ** * * *
3012 GTGTTGGGTTTTGGGGGGTGGTGG
124 GGGGGGGGGTGTGGGGGGGGGTGG
* * ** *
3036 GGGTGGGGGGTGGGGGGGGTGGTGGGGG-GGTGGGGTGGGGGGGT-GTGGTGGGGGGGGGTGTGG
1 GGGGGGGGGGTGGGGGGGGT--TGGGGGTGGGGGGGTGGGGGGGTGGTGGTGGTTGGGGGTGGGG
3099 TTGG
64 TTGG
3103 TGGTGTGTTG
Statistics
Matches: 179, Mismatches: 26, Indels: 24
0.78 0.11 0.10
Matches are distributed among these distances:
145 1 0.01
146 18 0.10
147 26 0.15
148 11 0.06
149 41 0.23
150 42 0.23
151 40 0.22
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (147 bp):
GGGGGGGGGGTGGGGGGGGTTGGGGGTGGGGGGGTGGGGGGGTGGTGGTGGTTGGGGGTGGGGTT
GGGGGGGGTTGGTGTGGGGTGGGGTGGGGGTGGGTGGTTGGGTGGGGGTGGGGTTGGGGGGGGGG
GGTGTGGGGGGGGGTGG
Found at i:3044 original size:16 final size:16
Alignment explanation
Indices: 2745--3099 Score: 161
Period size: 16 Copynumber: 21.0 Consensus size: 16
2735 TTTGTGGGGG
2745 GGGGGTGGGGGGTGGT
1 GGGGGTGGGGGGTGGT
*
2761 GTGTGGTGGGGGTGTGGT
1 G-GGGGTGGGGG-GTGGT
*
2779 GGTGGGTGGGGTTGGGGGT
1 GG-GGGTGGGG--GGTGGT
*
2798 GGGGTTGGGGGGGGTTGGT
1 GGGG--GTGGGGGG-TGGT
*
2817 GTGGGGTGGGGTGGGGGT
1 G-GGGGTGGGG-GGTGGT
*
2835 GGGTGTTTGGGTGGG-GGT
1 GGG-G-GTGGG-GGGTGGT
2853 -GGGGTGGGGGG-GG-
1 GGGGGTGGGGGGTGGT
*
2866 GGGGTGTGGGGGGGGGT
1 GGGG-GTGGGGGGTGGT
* *
2883 GGGTTGGGGGGGGGTGGG
1 GGG--GGTGGGGGGTGGT
*
2901 GGGGGTTGGGGGTGG-
1 GGGGGTGGGGGGTGGT
2916 GGGGGTGGGGGGGTGGT
1 GGGGGT-GGGGGGTGGT
* * *
2933 GGTGTGTTTGTGGTGTGGT
1 GG-G-G-GTGGGGGGTGGT
*
2952 -GTGGTGGGGGGTGGT
1 GGGGGTGGGGGGTGGT
*
2967 GTGGGGT-GGTGGTGGT
1 G-GGGGTGGGGGGTGGT
* * *
2983 TGGGGTGGTTGGTTGGTTT
1 GGGGGTGG-GGGGTGG--T
** *
3002 GGGGGT-TTGGGTGTT
1 GGGGGTGGGGGGTGGT
**
3017 GGGTTTTGGGGGGTGGT
1 GGG-GGTGGGGGGTGGT
*
3034 GGGGGTGGGGGGTGGG
1 GGGGGTGGGGGGTGGT
*
3050 GGGGGTGGTGGGGGGGT
1 GGGGGTGG-GGGGTGGT
*
3067 GGGGTGGGGGGGTGTGGT
1 GGGG-GTGGGGG-GTGGT
*
3085 GGGGG-GGGGTGTGGT
1 GGGGGTGGGGGGTGGT
3100 TGGTGGTGTG
Statistics
Matches: 259, Mismatches: 45, Indels: 71
0.69 0.12 0.19
Matches are distributed among these distances:
14 8 0.03
15 41 0.16
16 55 0.21
17 55 0.21
18 55 0.21
19 34 0.13
20 11 0.04
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (16 bp):
GGGGGTGGGGGGTGGT
Found at i:3081 original size:133 final size:126
Alignment explanation
Indices: 2891--3193 Score: 327
Period size: 128 Copynumber: 2.4 Consensus size: 126
2881 GTGGGTTGGG
* * *
2891 GGGGGGTGGGGGGGGTTGGGGGT-GGGGGGGTGG-GGGGGTGGTGGTGTGTTTGTGGTGTGGTGT
1 GGGGGGTGGTGGGGGTGGGGGGTGGGGGGGGTGGTGGGGG-GGTGG-G-G--TGTGG-GGGGTGT
* *
2954 GGTGGGGGGTGGTGTGGGGTGGTGGTG-GTTGGGGTGGTTGGTTGGT-T-TGGGGGTTTGGGTGT
60 GGTGGGGGGGGGTGT-GGGTGGTGGTGTGTT-GGGT--TTGGTGGGTGTGTGGGGG-TTGGGTG-
3016 TGGGTTTT
119 TGGGTTTT
3024 GGGGGGTGGTGGGGGTGGGGGGTGGGGGGGGTGGTGGGGGGGTGGGGTG-GGGGGGTGTGGTGGG
1 GGGGGGTGGTGGGGGTGGGGGGTGGGGGGGGTGGTGGGGGGGTGGGGTGTGGGGGGTGTGGTGGG
* *
3088 GGGGGGTGTGGTTGGTGGTGTGTTGGGTTTGGTGGGTGTGTGGGGGTTGGTTGTGGGTTTT
66 GGGGGGTGTGGGTGGTGGTGTGTTGGGTTTGGTGGGTGTGTGGGGGTTGGGTGTGGGTTTT
* * * *
3149 GGGTGGGT--TTGGTGTGGGGGGTGTGGGGGGT-GTGGGGGGTTGGGG
1 GGG-GGGTGGTGGGGGTGGGGGGTGGGGGGGGTGGTGGGGGGGTGGGG
3194 GGTTGGGTGG
Statistics
Matches: 153, Mismatches: 11, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
123 13 0.08
124 20 0.13
125 19 0.12
126 11 0.07
127 20 0.13
128 23 0.15
129 2 0.01
130 2 0.01
132 1 0.01
133 22 0.14
134 15 0.10
135 5 0.03
ACGTcount: A:0.00, C:0.00, G:0.70, T:0.30
Consensus pattern (126 bp):
GGGGGGTGGTGGGGGTGGGGGGTGGGGGGGGTGGTGGGGGGGTGGGGTGTGGGGGGTGTGGTGGG
GGGGGGTGTGGGTGGTGGTGTGTTGGGTTTGGTGGGTGTGTGGGGGTTGGGTGTGGGTTTT
Found at i:3098 original size:25 final size:25
Alignment explanation
Indices: 2737--3098 Score: 145
Period size: 25 Copynumber: 14.2 Consensus size: 25
2727 AAAATGGGTT
2737 TGTGGGGGGG-G-GGTGGGGGGTGGTG
1 TGTGGGGGGGTGTGGTGGGGGG-GG-G
2762 TGTGGTGGGGGTGTGGTGGTGGGTGGGG
1 TGTGG-GGGGGTGTGGTGG-GGG-GGGG
* *
2790 T-T--GGGGGTGGGGTTGGGGGGGG
1 TGTGGGGGGGTGTGGTGGGGGGGGG
* *
2812 T-TGGTGTGGGGTGGGGTGGGGGTGGG
1 TGTGG-G-GGGGTGTGGTGGGGGGGGG
* * *
2838 TGTTTGGGTGG-G-GGTGGGGTGGGG
1 TG-TGGGGGGGTGTGGTGGGGGGGGG
*
2862 -G-GGGGGGGTGTGGGGGGGGGTGGG
1 TGTGGGGGGGTGTGGTGGGGGG-GGG
*
2886 T-TGGGGGGGGGTGG-GGGGGGTTGGG
1 TGTGGGGGGGTGTGGTGGGGGG--GGG
*
2911 GGTGGGGGGGTG-GG-GGGGTGGTGGTG
1 TGTGGGGGGGTGTGGTGGGG-GG-GG-G
* *
2937 TGTTTGTGGTGTGGTGTGGTGGGGGGTGG
1 TG--TG-GG-GGGGTGTGGTGGGGGGGGG
* *
2966 TGTGGGGTGGTGGTGGTTGGGGTGGTTGG
1 TGTGGGGGGGT-GTGG-TGGGG-GG-GGG
**
2995 T-TGGTTTGGGGGT-T--TGGGTGTTGGG
1 TGTGG---GGGGGTGTGGTGGG-GGGGGG
**
3020 T-TTTGGGGG-GTGGTGGGGGTGGGG
1 TGTGGGGGGGTGTGGTGGGGG-GGGG
*
3044 GGTGGGGGGG-GTGGTGGGGGGGTGG
1 TGTGGGGGGGTGTGGTGGGGGGG-GG
*
3069 GGTGGGGGGGTGTGGTGGGGGGGGG
1 TGTGGGGGGGTGTGGTGGGGGGGGG
3094 TGTGG
1 TGTGG
3099 TTGGTGGTGT
Statistics
Matches: 266, Mismatches: 30, Indels: 82
0.70 0.08 0.22
Matches are distributed among these distances:
21 5 0.02
22 13 0.05
23 12 0.05
24 39 0.15
25 74 0.28
26 61 0.23
27 11 0.04
28 16 0.06
29 15 0.06
30 7 0.03
31 9 0.03
32 4 0.02
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (25 bp):
TGTGGGGGGGTGTGGTGGGGGGGGG
Found at i:3110 original size:29 final size:29
Alignment explanation
Indices: 2740--3095 Score: 135
Period size: 28 Copynumber: 12.3 Consensus size: 29
2730 ATGGGTTTGT
2740 GGGGGG-GGGGT-GGGGGGTGGTGTGTGGTG
1 GGGGGGTGGGGTGGGGGGGT-GTG-GTGGTG
* *
2769 GGGGTGTGGTGGTGGGTGGGGT-TGGGGGTG
1 GGGGGGTGG-GGTGGG-GGGGTGTGGTGGTG
* *
2799 GGGTTGGGGGGGGTTGGTGTGGGGTGGGGTGG-G
1 GGG--GGGTGGGG-TGG-G-GGGGTGTGGTGGTG
* **
2832 GGTGGGT-GTTTGGGTGGGG-GTGG-GGTG
1 GGGGGGTGGGGTGGG-GGGGTGTGGTGGTG
*
2859 GGGGGGGGGGGTGTGGGGGG-G-GGTGG-G
1 GGGGGGTGGGGTG-GGGGGGTGTGGTGGTG
* *
2886 TTGGGGG-GGGGTGGGGGGG-GTTGGGGGTG
1 -GGGGGGTGGGGTGGGGGGGTG-TGGTGGTG
* *
2915 GGGGGGTGGGG-GGGTGGTGGTGTGTTTGTG
1 GGGGGGTGGGGTGGG-GG-GGTGTGGTGGTG
* * *
2945 GTGTGGTGTGGT--GGGGG-GTGGT-GTG
1 GGGGGGTGGGGTGGGGGGGTGTGGTGGTG
* * *
2970 GGGTGGTGGTGGTTGGGGTGGT-TGGTTGGTTT
1 GGGGGGTGG-GG-TGGGGGGGTGTGG-TGG-TG
* * ** * * *
3002 GGGGGTTTGGGTGTTGGGTTTTGGGGGGTG
1 GGGGGGTGGGGTGGGGGGGTGT-GGTGGTG
3032 GTGGGGGTGGGG-GGTGGGGG-G-GGTGGTG
1 G-GGGGGTGGGGTGG-GGGGGTGTGGTGGTG
3060 GGGGGGTGGGGTGGGGGGGTGTGGTGG-G
1 GGGGGGTGGGGTGGGGGGGTGTGGTGGTG
3088 GGGGGGTG
1 GGGGGGTG
3096 TGGTTGGTGG
Statistics
Matches: 245, Mismatches: 45, Indels: 75
0.67 0.12 0.21
Matches are distributed among these distances:
25 10 0.04
26 15 0.06
27 36 0.15
28 54 0.22
29 30 0.12
30 35 0.14
31 28 0.11
32 18 0.07
33 15 0.06
34 4 0.02
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (29 bp):
GGGGGGTGGGGTGGGGGGGTGTGGTGGTG
Found at i:3120 original size:21 final size:20
Alignment explanation
Indices: 3091--3164 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 20
3081 TGGTGGGGGG
*
3091 GGGTGTGGTTGGTGGTGTGTT
1 GGGTTTGGTT-GTGGTGTGTT
*
3112 GGGTTTGG-TG-GGTGTGTG
1 GGGTTTGGTTGTGGTGTGTT
* *
3130 GGGGTTGGTTGTGG-GTTTT
1 GGGTTTGGTTGTGGTGTGTT
*
3149 GGG-TGGGTT-TGGTGTG
1 GGGTTTGGTTGTGGTGTG
3165 GGGGGTGTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.07
18 21 0.49
19 9 0.21
20 3 0.07
21 7 0.16
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (20 bp):
GGGTTTGGTTGTGGTGTGTT
Found at i:3171 original size:9 final size:9
Alignment explanation
Indices: 3159--3205 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
3149 GGGTGGGTTT
3159 GGTGTGGGG
1 GGTGTGGGG
3168 GGTGTGGGG
1 GGTGTGGGG
3177 GGTGTGGGG
1 GGTGTGGGG
3186 GGT-TGGGG
1 GGTGTGGGG
*
3194 GGT-TGGGT
1 GGTGTGGGG
3202 GGTG
1 GGTG
3206 GTTTGGGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
8 15 0.42
9 21 0.58
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (9 bp):
GGTGTGGGG
Found at i:3213 original size:12 final size:12
Alignment explanation
Indices: 2787--3231 Score: 75
Period size: 10 Copynumber: 39.2 Consensus size: 12
2777 GTGGTGGGTG
2787 GGGTTGGG-GGT
1 GGGTTGGGTGGT
2798 GGGGTTGGG-GG-
1 -GGGTTGGGTGGT
2809 GGGTT-GGT-GT
1 GGGTTGGGTGGT
*
2819 GGGGTGGGGTGG-
1 -GGGTTGGGTGGT
*
2831 GGG-TGGGTGTTT
1 GGGTTGGGTG-GT
2843 GGG-TGGG-GGT
1 GGGTTGGGTGGT
*
2853 GGGGTGGG-GG-
1 GGGTTGGGTGGT
*
2863 GGG-GGGGT-GT
1 GGGTTGGGTGGT
*
2873 GGG--GGGGGGT
1 GGGTTGGGTGGT
2883 GGGTTGGG-GG-
1 GGGTTGGGTGGT
*
2893 GGGGTGGG-GG-
1 GGGTTGGGTGGT
2903 GGGTTGGG-GGT
1 GGGTTGGGTGGT
* *
2914 GGG-GGGGTGGG
1 GGGTTGGGTGGT
*
2925 GGGGT-GGTGGT
1 GGGTTGGGTGGT
* *
2936 GTGTT-TGTGGT
1 GGGTTGGGTGGT
2947 GTGG-TGTGGTGG-
1 G-GGTTG-GGTGGT
*
2959 GGGGT-GGT-GT
1 GGGTTGGGTGGT
*
2969 GGGGT-GGTGGT
1 GGGTTGGGTGGT
2980 -GGTTGGGGTGGT
1 GGGTT-GGGTGGT
* *
2992 TGGTTGGTTTGG-
1 GGGTTGG-GTGGT
*
3004 GGGTTTGGGTGTT
1 GGG-TTGGGTGGT
*
3017 GGGTTTTGGGGGGT
1 GGG--TTGGGTGGT
3031 -GG-TGGG-GGT
1 GGGTTGGGTGGT
3040 GGG--GGGTGG-
1 GGGTTGGGTGGT
3049 GGG--GGGTGGT
1 GGGTTGGGTGGT
*
3059 GGG-GGGGTGGGGT
1 GGGTTGGGT--GGT
**
3072 GGGGGGGTGTGGT
1 GGGTTGG-GTGGT
*
3085 GGG--GGGGGGT
1 GGGTTGGGTGGT
3095 GTGGTT-GGTGGT
1 G-GGTTGGGTGGT
*
3107 GTGTTGGGTTTGGT
1 GGGTTGGG--TGGT
*
3121 GGG-TGTGTGG-
1 GGGTTGGGTGGT
*
3131 GGGTT-GGTTGT
1 GGGTTGGGTGGT
**
3142 GGGTTTTG-GGT
1 GGGTTGGGTGGT
*
3153 GGGTTTGGTGTGGG
1 GGG-TTGG-GTGGT
*
3167 GGGTGTGGGGGGT
1 GGGT-TGGGTGGT
* *
3180 GTGG-GGGGTTGGG
1 G-GGTTGGG-TGGT
3193 GGGTTGGGTGGT
1 GGGTTGGGTGGT
* *
3205 GGTTTGGGTTGT
1 GGGTTGGGTGGT
*
3217 GGGTTGGGGGGT
1 GGGTTGGGTGGT
3229 GGG
1 GGG
3232 GGTGGGGGGG
Statistics
Matches: 332, Mismatches: 48, Indels: 106
0.68 0.10 0.22
Matches are distributed among these distances:
9 26 0.08
10 82 0.25
11 68 0.20
12 79 0.24
13 48 0.14
14 27 0.08
15 2 0.01
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.29
Consensus pattern (12 bp):
GGGTTGGGTGGT
Found at i:3252 original size:8 final size:8
Alignment explanation
Indices: 3162--3253 Score: 62
Period size: 8 Copynumber: 10.6 Consensus size: 8
3152 TGGGTTTGGT
3162 GTGGGGGG
1 GTGGGGGG
3170 TGTGGGGGG
1 -GTGGGGGG
3179 TGTGGGGGG
1 -GTGGGGGG
*
3188 TTGGGGGG
1 GTGGGGGG
*
3196 TTGGGTGGTG
1 GTGGG-GG-G
3206 GTTTGGGTTGTGG
1 G--TGGG--G-GG
*
3219 GTTGGGGG
1 GTGGGGGG
3227 GT--GGGG
1 GTGGGGGG
3233 GTGGGGGG
1 GTGGGGGG
3241 GTGGGGGG
1 GTGGGGGG
3249 GTGGG
1 GTGGG
3254 TGTTGGGTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
6 6 0.08
8 33 0.46
9 20 0.28
10 1 0.01
11 3 0.04
12 4 0.06
13 4 0.06
14 1 0.01
ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25
Consensus pattern (8 bp):
GTGGGGGG
Found at i:3310 original size:12 final size:12
Alignment explanation
Indices: 3293--3319 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3283 CACCCCAACC
3293 AACCAACAAACA
1 AACCAACAAACA
3305 AACCAACAAACA
1 AACCAACAAACA
3317 AAC
1 AAC
3320 ACCCCCCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (12 bp):
AACCAACAAACA
Found at i:3620 original size:12 final size:12
Alignment explanation
Indices: 3605--3629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3595 ACAAATACAT
3605 TACAAAATGTAG
1 TACAAAATGTAG
3617 TACAAAATGTAG
1 TACAAAATGTAG
3629 T
1 T
3630 TATGAGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TACAAAATGTAG
Found at i:4703 original size:8 final size:8
Alignment explanation
Indices: 4690--4718 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4680 TAATTATTTT
4690 ATATAATA
1 ATATAATA
4698 ATATAATA
1 ATATAATA
4706 ATATAATA
1 ATATAATA
4714 ATATA
1 ATATA
4719 TAAAACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:4875 original size:15 final size:15
Alignment explanation
Indices: 4832--4879 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
4822 TTGATTATTA
*
4832 TTAATAAAATTATTAT
1 TTAATAAAATT-TAAT
* *
4848 CTAAAATAAATTTAAT
1 TTAATA-AAATTTAAT
4864 TTAATAAAATTTAAT
1 TTAATAAAATTTAAT
4879 T
1 T
4880 ATTTATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 10 0.38
16 11 0.42
17 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAATAAAATTTAAT
Found at i:4889 original size:26 final size:27
Alignment explanation
Indices: 4859--4911 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
4849 TAAAATAAAT
4859 TTAATTTAATAAA-ATTTAATTATTTA
1 TTAATTTAATAAATATTTAATTATTTA
* *
4885 TTAATTTCATAAATATTTTATTATTTA
1 TTAATTTAATAAATATTTAATTATTTA
4912 ATATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAATTTAATAAATATTTAATTATTTA
Found at i:4912 original size:24 final size:23
Alignment explanation
Indices: 4857--4947 Score: 64
Period size: 24 Copynumber: 3.8 Consensus size: 23
4847 TCTAAAATAA
*
4857 ATTTAATTTAATAAA-ATTTAATT
1 ATTTAATTT-ATAAATATTTTATT
4880 ATTTATTAATTTCATAAATATTTTATT
1 A--T-TTAATTT-ATAAATATTTTATT
*
4907 ATTTAATATA-AATATATTTTTATT
1 ATTTAATTTATAA-ATA-TTTTATT
*
4931 ATTT-A-TTATATATATTT
1 ATTTAATTTATAAATATTT
4948 ATTTTAATCG
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
21 3 0.05
22 7 0.12
23 7 0.12
24 17 0.30
25 2 0.04
26 12 0.21
27 8 0.14
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTAATTTATAAATATTTTATT
Found at i:4919 original size:21 final size:21
Alignment explanation
Indices: 4893--4947 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
4883 TATTAATTTC
4893 ATAAATATTTTATTATTTAAT
1 ATAAATATTTTATTATTTAAT
*
4914 ATAAATATATTTTTATTATTTATT
1 AT-AA-ATA-TTTTATTATTTAAT
*
4938 ATATATATTT
1 ATAAATATTT
4948 ATTTTAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 5 0.17
23 4 0.14
24 15 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATAAATATTTTATTATTTAAT
Found at i:5345 original size:69 final size:69
Alignment explanation
Indices: 5266--5401 Score: 263
Period size: 69 Copynumber: 2.0 Consensus size: 69
5256 TGGTTAAGTG
5266 ATAGTTTGAAAGGATAACAAATGAAATAAAATTATTATAAAAAATTTAAAATTAAAGGTACATAT
1 ATAGTTTGAAAGGATAACAAATGAAATAAAATTATTATAAAAAATTTAAAATTAAAGGTACATAT
5331 GTTA
66 GTTA
*
5335 ATAGTTTGAAAGGGTAACAAATGAAATAAAATTATTATAAAAAATTTAAAATTAAAGGTACATAT
1 ATAGTTTGAAAGGATAACAAATGAAATAAAATTATTATAAAAAATTTAAAATTAAAGGTACATAT
5400 GT
66 GT
5402 CTATTTTTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (69 bp):
ATAGTTTGAAAGGATAACAAATGAAATAAAATTATTATAAAAAATTTAAAATTAAAGGTACATAT
GTTA
Found at i:7903 original size:19 final size:19
Alignment explanation
Indices: 7858--7908 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
7848 TTTGATTCAA
7858 ATTAAAAAATATTCAAAATG
1 ATTAAAAAATATT-AAAATG
*
7878 ATT-AAAAATATTAACATTG
1 ATTAAAAAATATTAA-AATG
7897 -TTAAAAAA-ATTA
1 ATTAAAAAATATTA
7909 TTACAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.29
19 17 0.61
20 3 0.11
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATATTAAAATG
Found at i:9862 original size:33 final size:33
Alignment explanation
Indices: 9825--9889 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
9815 TTGAAGTTGC
*
9825 TCATATCTTCTTCTTTCTTCTTCTTTTGCTTCT
1 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
* *
9858 TCATATCTTCTTTTTTTTTCTTCTCTTGCTTC
1 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTC
9890 CTCTAACCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.65
Consensus pattern (33 bp):
TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
Found at i:10519 original size:98 final size:99
Alignment explanation
Indices: 10349--10549 Score: 300
Period size: 98 Copynumber: 2.0 Consensus size: 99
10339 CTATTTTTTC
* * *
10349 ACTTCGTTCTACTTCCTATAAAATAACATTTAATATGATATTTATATTGAAACATTAAAAATAAT
1 ACTTCGTTCCACTTCCTATAAAATAACATTTAATATGATATTTATATTAAAACAATAAAAATAAT
*
10414 AAAAATTTATTTTGAA-TTAAATCT-AGAAAACTT
66 AAAAATTTATTTT-AATTTAAATCTGAAAAAACTT
* *
10447 ACTTCGTTCCACTTCCTATAAAAT-ACAATTTAATATGGTATTTATATTAAAACAATAACAATAA
1 ACTTCGTTCCACTTCCTATAAAATAAC-ATTTAATATGATATTTATATTAAAACAATAAAAATAA
*
10511 TAACAATTTATTTTAATTTAAATCTGAAAAAACTT
65 TAAAAATTTATTTTAATTTAAATCTGAAAAAACTT
10546 ACTT
1 ACTT
10550 TCTCATATGC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
97 4 0.04
98 77 0.83
99 12 0.13
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.39
Consensus pattern (99 bp):
ACTTCGTTCCACTTCCTATAAAATAACATTTAATATGATATTTATATTAAAACAATAAAAATAAT
AAAAATTTATTTTAATTTAAATCTGAAAAAACTT
Found at i:13931 original size:21 final size:22
Alignment explanation
Indices: 13892--13933 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
13882 CAATTTTTAT
13892 ATATTTTTATAATTAAATAAAA
1 ATATTTTTATAATTAAATAAAA
13914 ATATTATTT-TAA-TAAATAAA
1 ATATT-TTTATAATTAAATAAA
13934 TAATTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTTTTATAATTAAATAAAA
Found at i:15338 original size:33 final size:34
Alignment explanation
Indices: 15267--15341 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 34
15257 GCTAAATGAT
15267 TTTATTTAACAGCATTTTCAATGCTGCTATATTA
1 TTTATTTAACAGCATTTTCAATGCTGCTATATTA
* *
15301 TTTATTTATCAGCATTTT-AATG-TCGCTATATTG
1 TTTATTTAACAGCATTTTCAATGCT-GCTATATTA
15334 TTTATTTA
1 TTTATTTA
15342 GCGGTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.53
34 17 0.45
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (34 bp):
TTTATTTAACAGCATTTTCAATGCTGCTATATTA
Found at i:15887 original size:5 final size:5
Alignment explanation
Indices: 15872--15911 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
15862 GAAAAAAAAA
*
15872 ATTAT ATTTAT ATTAT ATTAT ATTTAT ATTAA ATTAT ATT
1 ATTAT A-TTAT ATTAT ATTAT A-TTAT ATTAT ATTAT ATT
15912 TTATATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 21 0.68
6 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:15893 original size:16 final size:16
Alignment explanation
Indices: 15870--15918 Score: 80
Period size: 16 Copynumber: 3.0 Consensus size: 16
15860 GTGAAAAAAA
15870 AAATTATATTTATATT
1 AAATTATATTTATATT
*
15886 ATATTATATTTATATT
1 AAATTATATTTATATT
15902 AAATTATATTTTATATT
1 AAATTATA-TTTATATT
15919 TGATTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATTATATTTATATT
Found at i:15935 original size:22 final size:23
Alignment explanation
Indices: 15873--15939 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
15863 AAAAAAAAAA
*
15873 TTATATTTATATTATA--TTATAT
1 TTATA-TTAAATTATATTTTATAT
15895 TTATATTAAATTATATTTTATAT
1 TTATATTAAATTATATTTTATAT
*
15918 TTGAT-TT-AATTATTTTTTATAT
1 TT-ATATTAAATTATATTTTATAT
15940 AATATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.22
22 19 0.47
23 10 0.25
24 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
TTATATTAAATTATATTTTATAT
Found at i:16241 original size:32 final size:29
Alignment explanation
Indices: 16199--16268 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
16189 TTTTAAATTT
**
16199 AAAAATATAAAAGTAATTTTATATATATATA
1 AAAAATATAAAA--AATAATATATATATATA
*
16230 AAAAATTATAAAAAATAATATATTTATATA
1 AAAAA-TATAAAAAATAATATATATATATA
16260 AAAATATAT
1 AAAA-ATAT
16269 TTATATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 21 0.62
31 6 0.18
32 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAAATATAAAAAATAATATATATATATA
Found at i:16256 original size:18 final size:17
Alignment explanation
Indices: 16235--16273 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
16225 ATATAAAAAA
16235 TTATAAAAAATAATATAT
1 TTATAAAAAA-AATATAT
*
16253 TTAT-ATAAAAATATAT
1 TTATAAAAAAAATATAT
16269 TTATA
1 TTATA
16274 TTTAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.58
17 4 0.21
18 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATAAAAAAAATATAT
Found at i:16815 original size:2 final size:2
Alignment explanation
Indices: 16801--16862 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
16791 ATAAAGTAAG
* *
16801 TA TA TA T- TA -A TA TA TA TGA T- TT TA -A TA TA TA TC TA -A TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
16839 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
16863 CTAAAAGTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
1 5 0.10
2 44 0.86
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16894 original size:18 final size:18
Alignment explanation
Indices: 16871--16909 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
16861 TACTAAAAGT
16871 ATAAAAGTAATATATAAA
1 ATAAAAGTAATATATAAA
16889 ATAAAAGTAATATATAAA
1 ATAAAAGTAATATATAAA
16907 ATA
1 ATA
16910 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAAAAGTAATATATAAA
Found at i:17192 original size:40 final size:40
Alignment explanation
Indices: 17112--17194 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
17102 AATTTAATTC
* * **
17112 AATTTAAATTATTATTAATAATAAAAAATTATTTTATTTT
1 AATTTAAATTATTATGAATAATAAAAAAATAAATTATTTT
17152 AATTT-AATTATATATGAATAATAATAAAAATAAATT-TTTT
1 AATTTAAATTAT-TATGAATAATAA-AAAAATAAATTATTTT
17192 AAT
1 AAT
17195 ATTTTCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 6 0.16
40 23 0.62
41 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (40 bp):
AATTTAAATTATTATGAATAATAAAAAAATAAATTATTTT
Found at i:18061 original size:35 final size:34
Alignment explanation
Indices: 18022--18182 Score: 107
Period size: 35 Copynumber: 4.6 Consensus size: 34
18012 ATATATGTGA
*
18022 TAAATGATTAAAAATTATTAAAAATATATTTATAT
1 TAAAT-ATTAAAAATTATTAAAATTATATTTATAT
* * *
18057 TAAATAAT-AAAATAGAGATAAAATTATATTTATAT
1 TAAATATTAAAAAT-TA-TTAAAATTATATTTATAT
* * *
18092 TGAATAATAATTAAATT-TTATTAAATTATATTTATGT
1 TAAATATTAA--AAATTATTA--AAATTATATTTATAT
* * *
18129 TAAA-A--ATAAATTATTAGAATTATATTCATAT
1 TAAATATTAAAAATTATTAAAATTATATTTATAT
*
18160 TAAATAATAAAAAATATATTAAA
1 TAAAT-ATTAAAAAT-TATTAAA
18183 GACTAAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
31 16 0.16
32 5 0.05
33 9 0.09
34 4 0.04
35 35 0.36
36 8 0.08
37 17 0.17
38 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (34 bp):
TAAATATTAAAAATTATTAAAATTATATTTATAT
Found at i:18079 original size:73 final size:71
Alignment explanation
Indices: 18002--18138 Score: 161
Period size: 73 Copynumber: 1.9 Consensus size: 71
17992 AGTATTTGAT
*
18002 TAAAA-TAGATATATATGTG-ATAAATGATTAAAAATTATTAAAAATATATTTATATTAAATAAT
1 TAAAATTAGATATATAT-TGAAT-AATAATTAAAAATTATT-AAAATATATTTATATTAAA-AAT
18065 AAAATAGAGA
62 AAAATAGAGA
* * ** * *
18075 TAAAATTATATTTATATTGAATAATAATTAAATTTTATTAAATTATATTTATGTTAAAAATAAA
1 TAAAATTAGATATATATTGAATAATAATTAAAAATTATTAAAATATATTTATATTAAAAATAAA
18139 TTATTAGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
71 6 0.11
72 17 0.31
73 21 0.38
74 11 0.20
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (71 bp):
TAAAATTAGATATATATTGAATAATAATTAAAAATTATTAAAATATATTTATATTAAAAATAAAA
TAGAGA
Found at i:18150 original size:31 final size:31
Alignment explanation
Indices: 18033--18170 Score: 98
Period size: 37 Copynumber: 4.1 Consensus size: 31
18023 AAATGATTAA
* *
18033 AAATTATTAAAAATATATTTATATTAAATAAT
1 AAATTATT-AAATTATATTCATATTAAATAAT
* * *
18065 AAAATAGAGATAAAATTATATTTATATTGAATAATAATT
1 -AAAT---TATTAAATTATATTCATATT--A-AATAA-T
* *
18104 AAATTTTATTAAATTATATTTATGTTAAA-AAT
1 AAA--TTATTAAATTATATTCATATTAAATAAT
18136 AAATTATTAGAATTATATTCATATTAAATAAT
1 AAATTATTA-AATTATATTCATATTAAATAAT
18168 AAA
1 AAA
18171 AAATATATTA
Statistics
Matches: 86, Mismatches: 8, Indels: 23
0.74 0.07 0.20
Matches are distributed among these distances:
30 6 0.07
31 16 0.19
32 10 0.12
33 6 0.07
34 2 0.02
35 16 0.19
36 2 0.02
37 18 0.21
38 8 0.09
39 1 0.01
40 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.43
Consensus pattern (31 bp):
AAATTATTAAATTATATTCATATTAAATAAT
Found at i:22374 original size:22 final size:21
Alignment explanation
Indices: 22324--22374 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
22314 TGCACGGTTA
*
22324 ATATTTTAATATATAAAATTT
1 ATATTTTAATATATAAAAATT
*
22345 AT-TTTTAATTTATAAAAAATT
1 ATATTTTAATATAT-AAAAATT
*
22366 ATATATTAA
1 ATATTTTAA
22375 ATTAGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.40
21 10 0.40
22 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTTAATATATAAAAATT
Found at i:23127 original size:16 final size:17
Alignment explanation
Indices: 23108--23145 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
23098 ATATAGATAT
*
23108 AATATAAACATAATAC-
1 AATATAAAAATAATACG
23124 AATATAAAAATAATACG
1 AATATAAAAATAATACG
23141 AATAT
1 AATAT
23146 GATATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (17 bp):
AATATAAAAATAATACG
Found at i:23500 original size:41 final size:42
Alignment explanation
Indices: 23416--23508 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 42
23406 GCTAATAATA
23416 TTAATTAAAAACGTCACTAAATTATATTATATAACAACTTTT
1 TTAATTAAAAACGTCACTAAATTATATTATATAACAACTTTT
* * * **
23458 TTAATTAAAAATGTCA-TTAATTTTATTATATAATGA-TATTT
1 TTAATTAAAAACGTCACTAAATTATATTATATAACAACT-TTT
23499 TTAATTAAAA
1 TTAATTAAAA
23509 TACTGTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 1 0.02
41 29 0.64
42 15 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (42 bp):
TTAATTAAAAACGTCACTAAATTATATTATATAACAACTTTT
Found at i:23537 original size:104 final size:106
Alignment explanation
Indices: 23419--23613 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 106
23409 AATAATATTA
* * * *
23419 ATTAAAAACGTCACTAAATTATATTATATAACAACTTTTTTAATTAAAAATGTCATT-AATTTTA
1 ATTAAAAACATCACTAAATTATATCATACAAC-ACTTTTTTAATTAAAAATATCATTAAATTTTA
* *
23483 TTATATAATGATAT-T-TTTAATTAAAATACTGTTAAAAAAT
65 TCATATAACGATATCTCTTTAATTAAAATACTGTTAAAAAAT
* * *
23523 ATTAAAAATATCACTAAATTATATCATACAACAGTTTTTTAATTAAAAATATCGTTAAATTTTAT
1 ATTAAAAACATCACTAAATTATATCATACAACACTTTTTTAATTAAAAATATCATTAAATTTTAT
*
23588 CATATAGCGATATCTCTTTAATTAAA
66 CATATAACGATATCTCTTTAATTAAA
23614 CACCGTTACT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
103 21 0.27
104 46 0.59
105 1 0.01
106 10 0.13
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (106 bp):
ATTAAAAACATCACTAAATTATATCATACAACACTTTTTTAATTAAAAATATCATTAAATTTTAT
CATATAACGATATCTCTTTAATTAAAATACTGTTAAAAAAT
Found at i:25834 original size:32 final size:33
Alignment explanation
Indices: 25769--25841 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
25759 AAATTTGATG
*
25769 AAAGTTAACCAAACGTATATAATATCTAAGATC
1 AAAGTTAACCAAAAGTATATAATATCTAAGATC
*
25802 AAAGTTAACCAAAAGTATATAA-ATCTAGGATC
1 AAAGTTAACCAAAAGTATATAATATCTAAGATC
*
25834 AACGTTAA
1 AAAGTTAA
25842 TAGCTTCAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 16 0.43
33 21 0.57
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (33 bp):
AAAGTTAACCAAAAGTATATAATATCTAAGATC
Found at i:34018 original size:2 final size:2
Alignment explanation
Indices: 34011--34035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34001 TTCTGATTAC
34011 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34036 TAATTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35238 original size:41 final size:41
Alignment explanation
Indices: 35166--35246 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
35156 AAATCGATAA
*
35166 TTTTGTTTTGTTTTTTTGTTTTAATCAAATCTTTTGATTTC
1 TTTTGTTTTGTTTTTTTATTTTAATCAAATCTTTTGATTTC
*
35207 TTTT-TTTTGTTTTGTTTATTTTAATTAAATCTTTTGATTT
1 TTTTGTTTTGTTTT-TTTATTTTAATCAAATCTTTTGATTT
35247 TTTCTATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 9 0.24
41 28 0.76
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (41 bp):
TTTTGTTTTGTTTTTTTATTTTAATCAAATCTTTTGATTTC
Found at i:36927 original size:13 final size:13
Alignment explanation
Indices: 36909--36934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36899 CAATTTTTTG
36909 TGTATCGATACAT
1 TGTATCGATACAT
36922 TGTATCGATACAT
1 TGTATCGATACAT
36935 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36999 original size:21 final size:21
Alignment explanation
Indices: 36973--37048 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
36963 CTGCCAAGAA
*
36973 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
36994 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
37014 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
37035 ATGTATCGATACAT
1 ATGTATCGATACAT
37049 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:37019 original size:20 final size:20
Alignment explanation
Indices: 36994--37066 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
36984 CATCTTTTTT
36994 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
37014 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
37035 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
37055 ATGTATCGATAC
1 ATGTATCGATAC
37067 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:37030 original size:41 final size:41
Alignment explanation
Indices: 36973--37066 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
36963 CTGCCAAGAA
*
36973 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
37014 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
37055 ATGTATCGATAC
1 ATGTATCGATAC
37067 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:39525 original size:13 final size:13
Alignment explanation
Indices: 39507--39545 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
39497 ATAATCACCC
*
39507 TGTATCGATACAG
1 TGTATCGATACAA
39520 TGTATCGATACAA
1 TGTATCGATACAA
39533 TGTATCGATACAA
1 TGTATCGATACAA
39546 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:39556 original size:20 final size:20
Alignment explanation
Indices: 39531--39609 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
39521 GTATCGATAC
39531 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
39551 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
39576 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
39596 CATGTATCGATACA
1 AATGTATCGATACA
39610 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:41644 original size:15 final size:15
Alignment explanation
Indices: 41624--41654 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41614 ATTTCGTTTG
*
41624 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
41639 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
41654 G
1 G
41655 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:45734 original size:13 final size:13
Alignment explanation
Indices: 45716--45741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45706 CAATTTTTTG
45716 TGTATCGATACAT
1 TGTATCGATACAT
45729 TGTATCGATACAT
1 TGTATCGATACAT
45742 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:45806 original size:21 final size:21
Alignment explanation
Indices: 45780--45855 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
45770 CTGCCAAGAA
*
45780 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
45801 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
45821 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
45842 ATGTATCGATACAT
1 ATGTATCGATACAT
45856 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:45826 original size:20 final size:20
Alignment explanation
Indices: 45801--45873 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
45791 CATCTTTTTT
45801 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
45821 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
45842 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
45862 ATGTATCGATAC
1 ATGTATCGATAC
45874 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:45837 original size:41 final size:41
Alignment explanation
Indices: 45780--45873 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
45770 CTGCCAAGAA
*
45780 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
45821 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
45862 ATGTATCGATAC
1 ATGTATCGATAC
45874 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Done.