Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 6 of 345
Found at i:1939449 original size:66 final size:65
Alignment explanation
Indices: 1939343--1939508 Score: 226
Period size: 66 Copynumber: 2.5 Consensus size: 65
1939333 TGCTATGGTC
* * ** * *
1939343 GAATCAAATGCTCCTAACTAGA-TGTGATGAATGTGTCAAATAATTAGGATGGTATGATCGAAAT
1 GAATCAAATGCTCCTAATTAGAGTGTTATGAATGAATCAAATAACTAGGATGCTATGATCGAAAT
* * *
1939407 GAATCAAATGCTCTTAATTAAACGTGTTATGAATGAATCAAATAACTAGGATGCTATGATTGAAA
1 GAATCAAATGCTCCTAATTAGA-GTGTTATGAATGAATCAAATAACTAGGATGCTATGATCGAAA
1939472 T
65 T
1939473 GAATCAAATGCTCCTAATTAGATGTGTTATGAATGA
1 GAATCAAATGCTCCTAATTAGA-GTGTTATGAATGA
1939509 TGTATGAATG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 19 0.22
66 69 0.78
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (65 bp):
GAATCAAATGCTCCTAATTAGAGTGTTATGAATGAATCAAATAACTAGGATGCTATGATCGAAAT
Found at i:1945936 original size:46 final size:46
Alignment explanation
Indices: 1945883--1946058 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
1945873 TATTTGGGCA
1945883 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
1945929 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
1945976 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
1946022 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1946059 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:1946038 original size:93 final size:93
Alignment explanation
Indices: 1945879--1946050 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
1945869 GGGATATTTG
* *
1945879 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1945944 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
1945972 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1946037 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
1946051 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:1949023 original size:15 final size:15
Alignment explanation
Indices: 1949003--1949071 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
1948993 GTATCTTGGG
1949003 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
1949018 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
1949033 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
1949048 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
1949063 TTTCTTTAT
1 TTTCTTTAT
1949072 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:1949072 original size:30 final size:30
Alignment explanation
Indices: 1948994--1949081 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
1948984 CATAGTATCG
* * * *
1948994 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
1949024 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
1949054 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
1949082 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:1951512 original size:46 final size:46
Alignment explanation
Indices: 1951459--1951634 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
1951449 TATTTGGGCA
1951459 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
1951505 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* **
1951552 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
1951598 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1951635 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 65 0.60
47 32 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:1951614 original size:93 final size:93
Alignment explanation
Indices: 1951455--1951627 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
1951445 GGGATATTTG
* *
1951455 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1951520 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
1951548 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1951613 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
1951628 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:1955792 original size:19 final size:20
Alignment explanation
Indices: 1955768--1955811 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1955758 GGGTCTTTTC
* *
1955768 ATGAAATTTAATGCACATG-
1 ATGAAATGTAATGCAAATGA
1955787 ATGAAATGTAATGCAAATGA
1 ATGAAATGTAATGCAAATGA
1955807 ATGAA
1 ATGAA
1955812 TGCAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (20 bp):
ATGAAATGTAATGCAAATGA
Found at i:1959719 original size:23 final size:23
Alignment explanation
Indices: 1959693--1959743 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1959683 AAAAGAAAGA
1959693 AAAAAATAATATCAATAATGTAC
1 AAAAAATAATATCAATAATGTAC
1959716 AAAAAATAATATCAATAATGTAC
1 AAAAAATAATATCAATAATGTAC
1959739 AAAAA
1 AAAAA
1959744 TAGAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAAAATAATATCAATAATGTAC
Found at i:1960957 original size:44 final size:45
Alignment explanation
Indices: 1960867--1960995 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1960857 GACAGAACGA
*
1960867 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1960913 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1960957 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1960996 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1965868 original size:21 final size:22
Alignment explanation
Indices: 1965844--1965884 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1965834 TAAATTTTTA
*
1965844 AAATTTAAAAT-TTTTAAATAT
1 AAATTCAAAATATTTTAAATAT
*
1965865 AAATTCAATATATTTTAAAT
1 AAATTCAAAATATTTTAAAT
1965885 TTTAAATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTCAAAATATTTTAAATAT
Found at i:1998718 original size:2 final size:2
Alignment explanation
Indices: 1998711--1998740 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1998701 ATTGGTTTTA
1998711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1998741 TTAACGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2003296 original size:16 final size:18
Alignment explanation
Indices: 2003275--2003313 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2003265 TTAACAGCAT
2003275 TTCATATT-TTA-ATATG
1 TTCATATTATTACATATG
2003291 TTCATATTATTACATATG
1 TTCATATTATTACATATG
*
2003309 ATCAT
1 TTCAT
2003314 GTGATGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
TTCATATTATTACATATG
Found at i:2003443 original size:7 final size:7
Alignment explanation
Indices: 2003427--2003469 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
2003417 TTTTTTACCC
*
2003427 TAAATAT
1 TAAATTT
2003434 TAAATTT
1 TAAATTT
2003441 TAAATTT
1 TAAATTT
*
2003448 AAAATTT
1 TAAATTT
* *
2003455 TATATCT
1 TAAATTT
2003462 TAAATTT
1 TAAATTT
2003469 T
1 T
2003470 GACCCTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (7 bp):
TAAATTT
Found at i:2007472 original size:14 final size:14
Alignment explanation
Indices: 2007455--2007485 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2007445 GGATTTAGAG
2007455 TTTAAAGTTTAGGA
1 TTTAAAGTTTAGGA
2007469 TTTAAAGTTTAGGA
1 TTTAAAGTTTAGGA
2007483 TTT
1 TTT
2007486 TAAGATTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (14 bp):
TTTAAAGTTTAGGA
Found at i:2007497 original size:15 final size:14
Alignment explanation
Indices: 2007455--2007497 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2007445 GGATTTAGAG
*
2007455 TTTAAAGTTTAGGA
1 TTTAAAGTTCAGGA
*
2007469 TTTAAAGTTTAGGA
1 TTTAAAGTTCAGGA
*
2007483 TTTTAAGATTCAGGA
1 TTTAAAG-TTCAGGA
2007498 CAAGATCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (14 bp):
TTTAAAGTTCAGGA
Found at i:2020535 original size:26 final size:26
Alignment explanation
Indices: 2020498--2020559 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
2020488 GGTGCGACTC
*
2020498 TTTTTTTATATT-AA-AAAATATATAT
1 TTTTTTTTTATTAAATAAAATAT-TAT
2020523 TTTTTGTTTTATTAAATAAAATATTAT
1 TTTTT-TTTTATTAAATAAAATATTAT
2020550 TTTTTATTTT
1 TTTTT-TTTT
2020560 CGGATCAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 5 0.16
26 6 0.19
27 14 0.44
28 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTTTTTATTAAATAAAATATTAT
Found at i:2021487 original size:19 final size:21
Alignment explanation
Indices: 2021465--2021511 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
2021455 TTAATAAAAA
2021465 TAAAAAACAATATTTT-AT-T
1 TAAAAAACAATATTTTAATAT
**
2021484 TAAAAAATTATATTTTAATAT
1 TAAAAAACAATATTTTAATAT
2021505 TAAAAAA
1 TAAAAAA
2021512 AAGAGTCACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 2 0.08
21 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAACAATATTTTAATAT
Found at i:2022755 original size:14 final size:13
Alignment explanation
Indices: 2022736--2022777 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
2022726 ATTATATATT
2022736 TTAATTATGAAGAA
1 TTAATTAT-AAGAA
2022750 TTAATTA-AA-AA
1 TTAATTATAAGAA
*
2022761 TCAATTATAAGAA
1 TTAATTATAAGAA
2022774 TTAA
1 TTAA
2022778 AAATACATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 5 0.21
14 7 0.29
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (13 bp):
TTAATTATAAGAA
Found at i:2022811 original size:12 final size:11
Alignment explanation
Indices: 2022748--2022811 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 11
2022738 AATTATGAAG
2022748 AATTAATTAAA
1 AATTAATTAAA
*
2022759 AATCAATTATAA
1 AATTAATTA-AA
2022771 GAATTAA--AAA
1 -AATTAATTAAA
*
2022781 TACATTATTTAAA
1 -A-ATTAATTAAA
2022794 AATTAATTAAA
1 AATTAATTAAA
2022805 AAGTTAA
1 AA-TTAA
2022812 ACGTGTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
10 3 0.07
11 24 0.57
12 7 0.17
13 8 0.19
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (11 bp):
AATTAATTAAA
Found at i:2025368 original size:17 final size:18
Alignment explanation
Indices: 2025341--2025374 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2025331 GTGTTTTTGA
2025341 GATAAATAATATTTTTAG
1 GATAAATAATATTTTTAG
2025359 GATAAA-AATATTTTTA
1 GATAAATAATATTTTTA
2025375 AATAAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (18 bp):
GATAAATAATATTTTTAG
Found at i:2026334 original size:6 final size:6
Alignment explanation
Indices: 2026318--2026349 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2026308 TGTTTAAAAT
2026318 TTTAT- TTTATA TTTATA TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTT
2026350 TAATTTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTATA
Found at i:2027068 original size:19 final size:19
Alignment explanation
Indices: 2027029--2027068 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2027019 AAATTTTAAC
* * *
2027029 TTTTTACTCAAAAATATTT
1 TTTTTACACAAAAACAATT
2027048 TTTTTACACAAAAACAATT
1 TTTTTACACAAAAACAATT
2027067 TT
1 TT
2027069 AAAAAGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTTACACAAAAACAATT
Found at i:2028140 original size:30 final size:30
Alignment explanation
Indices: 2028104--2028195 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
2028094 AAAAAAATGG
* *
2028104 CAGAGAAGATCAGTGATGAAACCCCAAATC
1 CAGAGAAGATCAATGATGAATCCCCAAATC
2028134 CAGAGAAGATCAATGATGAATCCCCAAATC
1 CAGAGAAGATCAATGATGAATCCCCAAATC
*
2028164 CAGAGAAAATCAATGATGAATCCCCAAATC
1 CAGAGAAGATCAATGATGAATCCCCAAATC
2028194 CA
1 CA
2028196 TTGGCACCAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (30 bp):
CAGAGAAGATCAATGATGAATCCCCAAATC
Found at i:2029948 original size:18 final size:18
Alignment explanation
Indices: 2029919--2029960 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2029909 GTTCTTATTA
2029919 TAATTT-TTTAATAATTT
1 TAATTTCTTTAATAATTT
*
2029936 TAATTTCTTTAATATTTT
1 TAATTTCTTTAATAATTT
*
2029954 TAGTTTC
1 TAATTTC
2029961 AATTTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (18 bp):
TAATTTCTTTAATAATTT
Found at i:2030280 original size:13 final size:13
Alignment explanation
Indices: 2030262--2030286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2030252 CAACTTTATC
2030262 ATCGAAGTAACAA
1 ATCGAAGTAACAA
2030275 ATCGAAGTAACA
1 ATCGAAGTAACA
2030287 CCAGCTCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
ATCGAAGTAACAA
Found at i:2031336 original size:77 final size:79
Alignment explanation
Indices: 2031233--2031385 Score: 229
Period size: 79 Copynumber: 1.9 Consensus size: 79
2031223 TCATACTACT
* * *
2031233 CTTTCGATACACAATCTAATGTTTTG-AAAAAAAAGATATCAAAAAAAAAATTTATATCGAATTT
1 CTTTCGATACACAATCTAATATTTTGAAAAAAAAAGAAATCAAAAAAAAAATATATATCGAATTT
2031297 GAAGTGCCATGCTC
66 GAAGTGCCATGCTC
* * *
2031311 CTTT-GATACACAATTTAATATTTTGAAAAAAAAAAGAAATCAAAAAATATATATATATCGAATT
1 CTTTCGATACACAATCTAATATTTTG-AAAAAAAAAGAAATCAAAAAAAAAATATATATCGAATT
2031375 TGAAGTGCCAT
65 TGAAGTGCCAT
2031386 ACTATTATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 19 0.28
78 4 0.06
79 44 0.66
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (79 bp):
CTTTCGATACACAATCTAATATTTTGAAAAAAAAAGAAATCAAAAAAAAAATATATATCGAATTT
GAAGTGCCATGCTC
Found at i:2036891 original size:22 final size:22
Alignment explanation
Indices: 2036865--2036906 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2036855 TTTAATATTC
*
2036865 AATTTGATAT-TTAAATTTTTTT
1 AATTTAATATATT-AATTTTTTT
2036887 AATTTAATATATTAATTTTT
1 AATTTAATATATTAATTTTT
2036907 CTCCCAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
AATTTAATATATTAATTTTTTT
Found at i:2037017 original size:30 final size:29
Alignment explanation
Indices: 2036983--2037046 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
2036973 TTAAATAAGA
2036983 TTTTTTTTAAAAATTTAATC-ATATATGCCT
1 TTTTTTTTAAAAATTT-ATCGATATATG-CT
*
2037013 TTTTTTTTATAAATTTATCGATATATGCT
1 TTTTTTTTAAAAATTTATCGATATATGCT
2037042 TTTTT
1 TTTTT
2037047 CATTGTCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (29 bp):
TTTTTTTTAAAAATTTATCGATATATGCT
Found at i:2039189 original size:6 final size:6
Alignment explanation
Indices: 2039180--2039214 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2039170 TTAAGGTAAA
2039180 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAA
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAA
2039215 ATGACAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (6 bp):
GGCAAT
Found at i:2040070 original size:11 final size:11
Alignment explanation
Indices: 2040051--2040079 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2040041 AGGGTTCTTT
2040051 TTTTC-TTTTC
1 TTTTCTTTTTC
2040061 TTTTCTTTTTC
1 TTTTCTTTTTC
2040072 TTTTCTTT
1 TTTTCTTT
2040080 CTTAGATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:2042675 original size:22 final size:24
Alignment explanation
Indices: 2042648--2042700 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
2042638 ACAATTTAAA
2042648 ATATAAAAATTTATT-A-ATATGT
1 ATATAAAAATTTATTAATATATGT
2042670 ATAT--AAATTTATTAATATATGT
1 ATATAAAAATTTATTAATATATGT
2042692 A-ATAAAAAT
1 ATATAAAAAT
2042701 AATTTTTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 9 0.33
21 3 0.11
22 11 0.41
23 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATAAAAATTTATTAATATATGT
Found at i:2042677 original size:20 final size:20
Alignment explanation
Indices: 2042649--2042687 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2042639 CAATTTAAAA
2042649 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
2042669 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
2042688 ATGTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:2042819 original size:20 final size:20
Alignment explanation
Indices: 2042790--2042828 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2042780 ATATTTTCAG
2042790 TAAATCATTTTCCAGAAAAA
1 TAAATCATTTTCCAGAAAAA
* *
2042810 TAAATTATTTTTCAGAAAA
1 TAAATCATTTTCCAGAAAA
2042829 CATTTTACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAA
Found at i:2044923 original size:16 final size:18
Alignment explanation
Indices: 2044884--2044923 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2044874 TAATTTACTC
2044884 TTTAATTTAATATATAAT
1 TTTAATTTAATATATAAT
2044902 TATTAATTT-ATATAT-AT
1 T-TTAATTTAATATATAAT
2044919 TTTAA
1 TTTAA
2044924 ATAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 3 0.14
18 7 0.33
19 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATTTAATATATAAT
Found at i:2045500 original size:21 final size:21
Alignment explanation
Indices: 2045459--2045499 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2045449 TATATCACAT
*
2045459 TATTATTTAAAAATTTTAAAA
1 TATTATATAAAAATTTTAAAA
2045480 TATTATAT-AAAATTTTAAAA
1 TATTATATAAAAATTTTAAAA
2045500 AGTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTATATAAAAATTTTAAAA
Found at i:2047572 original size:94 final size:95
Alignment explanation
Indices: 2047421--2047594 Score: 289
Period size: 94 Copynumber: 1.8 Consensus size: 95
2047411 GCGTTGATGA
* *
2047421 ACGAATGCATTTTCAAATCTGTAATTTGAATAATATTACGAGTTGATGAAATATTGTTT-AATTC
1 ACGAATGCATTTTCAAATCTGTAATTTGAATAATAGTACAAGTTGATGAAATATTGTTTAAATTC
*
2047485 CTCAATTGATATTTCAATGAAATTGCGTTG
66 CTCAATTGAGATTTCAATGAAATTGCGTTG
*
2047515 ACGAATGCATCTTT-AAATCTGTAATTTGAATAATAGTACAAGTTGATGAAATCTTGTTTAAATT
1 ACGAATGCAT-TTTCAAATCTGTAATTTGAATAATAGTACAAGTTGATGAAATATTGTTTAAATT
2047579 CCTCAATTGAGATTTC
65 CCTCAATTGAGATTTC
2047595 TTAACAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
94 52 0.70
95 22 0.30
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (95 bp):
ACGAATGCATTTTCAAATCTGTAATTTGAATAATAGTACAAGTTGATGAAATATTGTTTAAATTC
CTCAATTGAGATTTCAATGAAATTGCGTTG
Found at i:2048504 original size:32 final size:32
Alignment explanation
Indices: 2048467--2048565 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 32
2048457 TTTTAAAGTA
2048467 TTAAATGTTAGTAATTTGAATCTAACAATATT
1 TTAAATGTTAGTAATTTGAATCTAACAATATT
* * * * * * *
2048499 TTAAATATAATTAATGTG--TTTTA-AATATG
1 TTAAATGTTAGTAATTTGAATCTAACAATATT
* *
2048528 CTAAATGTTAGTAGTTTGAATCTAACAATATT
1 TTAAATGTTAGTAATTTGAATCTAACAATATT
2048560 TTAAAT
1 TTAAAT
2048566 ATAATTAATG
Statistics
Matches: 47, Mismatches: 17, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
29 17 0.36
30 3 0.06
31 3 0.06
32 24 0.51
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.44
Consensus pattern (32 bp):
TTAAATGTTAGTAATTTGAATCTAACAATATT
Found at i:2048533 original size:61 final size:60
Alignment explanation
Indices: 2048448--2048589 Score: 236
Period size: 61 Copynumber: 2.4 Consensus size: 60
2048438 CAAAATGTTC
2048448 TAATTAA-GT-TTTTAAAGTAT-TAAATGTTAGTAATTTGAATCTAACAATATTTTAAATA
1 TAATTAATGTGTTTTAAA-TATGTAAATGTTAGTAATTTGAATCTAACAATATTTTAAATA
*
2048506 TAATTAATGTGTTTTAAATATGCTAAATGTTAGTAGTTTGAATCTAACAATATTTTAAATA
1 TAATTAATGTGTTTTAAATATG-TAAATGTTAGTAATTTGAATCTAACAATATTTTAAATA
2048567 TAATTAATGTGTTTTAAATATGT
1 TAATTAATGTGTTTTAAATATGT
2048590 TTTATGTCAT
Statistics
Matches: 79, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
58 7 0.09
59 5 0.06
60 8 0.10
61 59 0.75
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (60 bp):
TAATTAATGTGTTTTAAATATGTAAATGTTAGTAATTTGAATCTAACAATATTTTAAATA
Found at i:2048596 original size:20 final size:20
Alignment explanation
Indices: 2048497--2048587 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
2048487 TCTAACAATA
2048497 TTTTAAATATAATTAATGTG
1 TTTTAAATATAATTAATGTG
** *
2048517 TTTTAAATATGCTAAATGTTAG
1 TTTTAAATATAATTAATG-T-G
* * * *
2048539 TAGTTTGAATCTAA-CAA--TA
1 T--TTTAAATATAATTAATGTG
2048558 TTTTAAATATAATTAATGTG
1 TTTTAAATATAATTAATGTG
2048578 TTTTAAATAT
1 TTTTAAATAT
2048588 GTTTTATGTC
Statistics
Matches: 51, Mismatches: 13, Indels: 14
0.65 0.17 0.18
Matches are distributed among these distances:
17 9 0.18
18 2 0.04
19 1 0.02
20 27 0.53
21 1 0.02
22 2 0.04
23 2 0.04
24 7 0.14
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTTAAATATAATTAATGTG
Found at i:2065300 original size:17 final size:17
Alignment explanation
Indices: 2065268--2065301 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2065258 ATTATCTTGA
*
2065268 ATTTTTTGAATGTTTTC
1 ATTTTTTGAATATTTTC
*
2065285 ATTTTTTGTATATTTTC
1 ATTTTTTGAATATTTTC
2065302 GATCAGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.68
Consensus pattern (17 bp):
ATTTTTTGAATATTTTC
Found at i:2069091 original size:88 final size:88
Alignment explanation
Indices: 2068942--2069117 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
2068932 AACTTTCGAA
2068942 TGATTGTCACTTCTTCTACTTCTTCTTCTTCTTTTTATTTATTTTTATTTTACTTTTATTGAATC
1 TGATTGTCACTTCTTCTACTTCTTCTTCTTCTTTTTATTTATTTTTATTTTACTTTTATTGAATC
2069007 TGATGAAGTTCATGAAACCCATT
66 TGATGAAGTTCATGAAACCCATT
2069030 TGATTGTCACTTCTTCTACTTCTTCTTCTTCTTTTTATTTATTTTTATTTTACTTTTATTGAATC
1 TGATTGTCACTTCTTCTACTTCTTCTTCTTCTTTTTATTTATTTTTATTTTACTTTTATTGAATC
2069095 TGATGAAGTTCATGAAACCCATT
66 TGATGAAGTTCATGAAACCCATT
2069118 CCTGCAGCTT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (88 bp):
TGATTGTCACTTCTTCTACTTCTTCTTCTTCTTTTTATTTATTTTTATTTTACTTTTATTGAATC
TGATGAAGTTCATGAAACCCATT
Found at i:2071541 original size:3 final size:3
Alignment explanation
Indices: 2071533--2071580 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2071523 TTTAAATCTT
2071533 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2071581 CCTTCACTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2079562 original size:21 final size:21
Alignment explanation
Indices: 2079536--2079576 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2079526 GTACTTGTTT
*
2079536 TGGTCAAAATTGGAGTCCTTA
1 TGGTCAAAATTGGAGGCCTTA
2079557 TGGTCAAAATTGGAGGCCTT
1 TGGTCAAAATTGGAGGCCTT
2079577 CTGTTTAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (21 bp):
TGGTCAAAATTGGAGGCCTTA
Found at i:2093185 original size:2 final size:2
Alignment explanation
Indices: 2093178--2093204 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2093168 GTTAGGTATA
2093178 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2093205 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2094205 original size:16 final size:17
Alignment explanation
Indices: 2094179--2094213 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2094169 AATGCATATA
*
2094179 GAAATAGAAGATGATTG
1 GAAATAGAAGATAATTG
2094196 GAAA-AGAAGATAATTG
1 GAAATAGAAGATAATTG
2094212 GA
1 GA
2094214 TAGTGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (17 bp):
GAAATAGAAGATAATTG
Found at i:2095394 original size:28 final size:28
Alignment explanation
Indices: 2095333--2095401 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 28
2095323 GTCAGTAATT
2095333 TAATATAAATATAAATAATAATTATTTA
1 TAATATAAATATAAATAATAATTATTTA
*
2095361 -ACATATATAAT-TAATATAAT-ATTTTTTA
1 TA-ATATA-AATATAA-ATAATAATTATTTA
2095389 TAATATAATATAT
1 TAATATAA-ATAT
2095402 TTGGGTTGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
27 2 0.06
28 22 0.65
29 10 0.29
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATATAAATATAAATAATAATTATTTA
Found at i:2098342 original size:13 final size:13
Alignment explanation
Indices: 2098324--2098349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2098314 AACTGTTGGA
2098324 ACAACCTTATTTC
1 ACAACCTTATTTC
2098337 ACAACCTTATTTC
1 ACAACCTTATTTC
2098350 CAGGAGACAT
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:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACAACCTTATTTC
Found at i:2112731 original size:26 final size:26
Alignment explanation
Indices: 2112700--2112751 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2112690 CTTGAGATTC
2112700 ATAAACATTTATACATATAATTCATT
1 ATAAACATTTATACATATAATTCATT
2112726 ATAAACATTTATACATATAATTCATT
1 ATAAACATTTATACATATAATTCATT
2112752 TCATCTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAAACATTTATACATATAATTCATT
Found at i:2115433 original size:14 final size:15
Alignment explanation
Indices: 2115414--2115442 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2115404 TCTTTACAGT
2115414 TAAATAAAAA-TAAA
1 TAAATAAAAACTAAA
2115428 TAAATAAAAACTAAA
1 TAAATAAAAACTAAA
2115443 CCAACCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAATAAAAACTAAA
Found at i:2129083 original size:3 final size:3
Alignment explanation
Indices: 2129075--2129112 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2129065 GTCATGTGCC
2129075 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2129113 TTACTATACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2138151 original size:17 final size:18
Alignment explanation
Indices: 2138105--2138151 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2138095 TTACCTAATT
*
2138105 AATTCTTTTAATTCACCA
1 AATTCTTCTAATTCACCA
* *
2138123 AATTC-ACCAATTCA-CA
1 AATTCTTCTAATTCACCA
2138139 AATTCTTCTAATT
1 AATTCTTCTAATT
2138152 TCTCACTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTCTTCTAATTCACCA
Found at i:2148435 original size:24 final size:24
Alignment explanation
Indices: 2148408--2148456 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2148398 TAAAAACCTA
2148408 CACGACCCCTTATAAAAAAAACAC
1 CACGACCCCTTATAAAAAAAACAC
2148432 CACGACCCCTTATAAAAAAAACAC
1 CACGACCCCTTATAAAAAAAACAC
2148456 C
1 C
2148457 CAAGACATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.35, G:0.04, T:0.12
Consensus pattern (24 bp):
CACGACCCCTTATAAAAAAAACAC
Found at i:2150211 original size:31 final size:32
Alignment explanation
Indices: 2150163--2150238 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 32
2150153 TAAAAGAACC
* * *
2150163 ATAT-AAAATATATAAATAT-TTTTTAA-AAA
1 ATATAAAAATAAAAAAATATATTTTCAAGAAA
2150192 TATATAAAAATAAAAAAATATAATTTTCAAGAAA
1 -ATATAAAAATAAAAAAATAT-ATTTTCAAGAAA
*
2150226 ATATAATAATAAA
1 ATATAAAAATAAA
2150239 TTTTAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 4 0.11
31 13 0.34
33 18 0.47
34 3 0.08
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (32 bp):
ATATAAAAATAAAAAAATATATTTTCAAGAAA
Found at i:2151406 original size:83 final size:85
Alignment explanation
Indices: 2151264--2151431 Score: 202
Period size: 83 Copynumber: 2.0 Consensus size: 85
2151254 CAGAATTAAA
* * *
2151264 TTATATATTTTTATAATAGTAAAAATATAATTACATTATTTTAATAATTTATATCTTTATAATTT
1 TTATATATTTTTATAAAAGTAAAAATATAATT--ATTATTTTAATAATTTAAATCTTTATAAATT
* *
2151329 TTAAATAAT-TAAATTAAAATT
64 ATAAATAATCTAAATAAAAATT
*
2151350 TTAT-TATTTTT-TAAAAGATAAAAATATAATT-TTATCTTTACTAATTTAAAAT-TTTATAAAT
1 TTATATATTTTTATAAAAG-TAAAAATATAATTATTAT-TTTAATAATTT-AAATCTTTATAAAT
2151411 TATAAATAATCTAAATAAAAA
63 TATAAATAATCTAAATAAAAA
2151432 AAATTCTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
82 4 0.06
83 27 0.38
84 17 0.24
85 20 0.28
86 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (85 bp):
TTATATATTTTTATAAAAGTAAAAATATAATTATTATTTTAATAATTTAAATCTTTATAAATTAT
AAATAATCTAAATAAAAATT
Found at i:2153017 original size:31 final size:31
Alignment explanation
Indices: 2152979--2153037 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2152969 AATTATCGTT
* *
2152979 AAACTATTTGAAA-GTTTTTATTTAAGTCCCA
1 AAACTATTCGAAATG-TTTTACTTAAGTCCCA
2153010 AAACTATTCGAAATGTTTTACTTAAGTC
1 AAACTATTCGAAATGTTTTACTTAAGTC
2153038 ACTAAGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (31 bp):
AAACTATTCGAAATGTTTTACTTAAGTCCCA
Found at i:2157376 original size:47 final size:47
Alignment explanation
Indices: 2157312--2157422 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
2157302 GACATTGAGT
*
2157312 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
2157359 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
2157406 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
2157423 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:2162279 original size:12 final size:13
Alignment explanation
Indices: 2162245--2162284 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2162235 TTTTTTTAAG
2162245 TAGTTTATTGATA
1 TAGTTTATTGATA
2162258 TAGTCATTATT-ATA
1 TAGT--TTATTGATA
2162272 TAGTTTATTGATA
1 TAGTTTATTGATA
2162285 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 7 0.29
15 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TAGTTTATTGATA
Found at i:2166036 original size:46 final size:46
Alignment explanation
Indices: 2165984--2166196 Score: 300
Period size: 46 Copynumber: 4.6 Consensus size: 46
2165974 TGCCGTAGTG
* * ** *
2165984 TCTTTCAACTATGGTCTTACTCATTTTTTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
* ** * * *
2166030 TCTTTCAACCATAGTCTTATTCATTTCATGTCACGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
*
2166076 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGTCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
* *
2166122 TCTTTCAACCATAGTTTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
2166168 TCTTTCAACCATGGTCTTACACATTTCAT
1 TCTTTCAACCATGGTCTTACACATTTCAT
2166197 TTCAGAGAGC
Statistics
Matches: 148, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 148 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
Found at i:2167558 original size:53 final size:54
Alignment explanation
Indices: 2167432--2167562 Score: 174
Period size: 53 Copynumber: 2.4 Consensus size: 54
2167422 ATGGCCGACA
* * * * *
2167432 CGTATTTTGGTGCCGACCATTGACATGCCAGCACCAATTTTTTTTTTTTAAAACT
1 CGTATTTTGGTGCCGGCCATTGACACGCCAACACCAA-TATTTTTTTTGAAAACT
* *
2167487 TGTATTTTGATGCCGGCCATTGACACGCCAACACCAA-ATTTTTTTTGAAAACT
1 CGTATTTTGGTGCCGGCCATTGACACGCCAACACCAATATTTTTTTTGAAAACT
*
2167540 CGTATTTTGGTGCTGGCCATTGA
1 CGTATTTTGGTGCCGGCCATTGA
2167563 TAAACCAGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
53 34 0.52
55 32 0.48
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (54 bp):
CGTATTTTGGTGCCGGCCATTGACACGCCAACACCAATATTTTTTTTGAAAACT
Found at i:2168103 original size:33 final size:31
Alignment explanation
Indices: 2168033--2168108 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
2168023 AGACCACTAG
* * *
2168033 TAAT-TTTATCATATACATATGTATGAAAAT
1 TAATATTTATAATATAAATATGTATGAAAAC
*
2168063 TATATATTTATAATATAAATATGTGTTGAAAAAC
1 TA-ATATTTATAATATAAATATGT-ATG-AAAAC
*
2168097 TAATATTAATAA
1 TAATATTTATAA
2168109 ATTAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.05
31 2 0.05
32 16 0.43
33 11 0.30
34 6 0.16
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (31 bp):
TAATATTTATAATATAAATATGTATGAAAAC
Found at i:2168864 original size:19 final size:18
Alignment explanation
Indices: 2168825--2168859 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2168815 TGTTGTTTAA
2168825 TAAAAATGAATATTAATT
1 TAAAAATGAATATTAATT
*
2168843 TAAAAA-GATTATTAATT
1 TAAAAATGAATATTAATT
2168860 ATTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TAAAAATGAATATTAATT
Found at i:2168885 original size:21 final size:22
Alignment explanation
Indices: 2168851--2168897 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
2168841 TTTAAAAAGA
* *
2168851 TTATTAATTATTAATTTTAATC
1 TTATTAATTATTAATATTAATA
2168873 TTATTAA-TATTAATATTAATA
1 TTATTAATTATTAATATTAATA
2168894 TTAT
1 TTAT
2168898 ATTATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTAATTATTAATATTAATA
Found at i:2183330 original size:22 final size:22
Alignment explanation
Indices: 2183304--2183368 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
2183294 ATATCCAAAC
2183304 AATAACAATAAAATAGTAGTAA
1 AATAACAATAAAATAGTAGTAA
* * ** *
2183326 TATAATAATAAAATAACATTAA
1 AATAACAATAAAATAGTAGTAA
* *
2183348 AACAACAACAAAATAGTAGTA
1 AATAACAATAAAATAGTAGTA
2183369 GAAAAAAATT
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGTAA
Found at i:2183966 original size:53 final size:53
Alignment explanation
Indices: 2183897--2184005 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
2183887 CATATGATAA
2183897 TTTTATATATGGTTGACAAAGGAAGGGTAATAATTTATCACCATGATGCTTGC
1 TTTTATATATGGTTGACAAAGGAAGGGTAATAATTTATCACCATGATGCTTGC
2183950 TTTTATATATGGTTGACAAAGGAAGGGTAATAATTTATCACCATGATGCTTGC
1 TTTTATATATGGTTGACAAAGGAAGGGTAATAATTTATCACCATGATGCTTGC
2184003 TTT
1 TTT
2184006 AAGGTAACAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (53 bp):
TTTTATATATGGTTGACAAAGGAAGGGTAATAATTTATCACCATGATGCTTGC
Found at i:2184997 original size:16 final size:17
Alignment explanation
Indices: 2184976--2185044 Score: 58
Period size: 16 Copynumber: 4.3 Consensus size: 17
2184966 TTATATTTTG
2184976 ATATTAATT-TTTTAAA
1 ATATTAATTATTTTAAA
*
2184992 ATATTAATTATTTTAGA
1 ATATTAATTATTTTAAA
* *
2185009 ATA--ATTTATATT--A
1 ATATTAATTATTTTAAA
*
2185022 ATGTTAATTTATTTTAAA
1 ATATTAA-TTATTTTAAA
2185040 ATATT
1 ATATT
2185045 TAATATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
13 3 0.08
15 8 0.20
16 15 0.38
17 9 0.22
18 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATATTAATTATTTTAAA
Found at i:2185029 original size:30 final size:31
Alignment explanation
Indices: 2184995--2185053 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2184985 TTTTAAAATA
*
2184995 TTAA-TTATTTTAGAATAATTT-ATATTAATG
1 TTAATTTATTTTAAAAT-ATTTAATATTAATG
2185025 TTAATTTATTTTAAAATATTTAATATTAA
1 TTAATTTATTTTAAAATATTTAATATTAA
2185054 AATAATACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TTAATTTATTTTAAAATATTTAATATTAATG
Found at i:2185106 original size:19 final size:19
Alignment explanation
Indices: 2185082--2185120 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2185072 CATGGTTTCA
*
2185082 ATATTAATATTAATATATT
1 ATATTAATAATAATATATT
* *
2185101 ATATTATTAATAATTTATT
1 ATATTAATAATAATATATT
2185120 A
1 A
2185121 CATGTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAATAATAATATATT
Found at i:2193191 original size:23 final size:25
Alignment explanation
Indices: 2193165--2193221 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2193155 CATTGATAAG
2193165 TATAATTTTA-T-TTTATATT-AATT
1 TATAATTTTATTATTTAT-TTAAATT
*
2193188 TATAATTTCATTATTTATTTAAATT
1 TATAATTTTATTATTTATTTAAATT
*
2193213 TAAAATTTT
1 TATAATTTT
2193222 CCATTTTCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.32
24 3 0.11
25 16 0.57
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATAATTTTATTATTTATTTAAATT
Found at i:2201158 original size:9 final size:9
Alignment explanation
Indices: 2201116--2201164 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
2201106 TTTTATTGAG
*
2201116 AATTTTCAA
1 AATTTTTAA
2201125 AATTTTTAA
1 AATTTTTAA
* *
2201134 AATCTAATTGA
1 AAT-T-TTTAA
2201145 AATTTTTAA
1 AATTTTTAA
2201154 AATTTTTAA
1 AATTTTTAA
2201163 AA
1 AA
2201165 GTTAACTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 25 0.76
10 2 0.06
11 6 0.18
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (9 bp):
AATTTTTAA
Found at i:2210268 original size:20 final size:20
Alignment explanation
Indices: 2210245--2210284 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2210235 CAAATGTGTT
*
2210245 AAAATTATTAATTAAAAATA
1 AAAAATATTAATTAAAAATA
*
2210265 AAAAATATTAATTACAAATA
1 AAAAATATTAATTAAAAATA
2210285 TTTAATGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATATTAATTAAAAATA
Found at i:2210365 original size:24 final size:24
Alignment explanation
Indices: 2210338--2210383 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2210328 CTAATTAAAT
* *
2210338 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
2210362 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
2210384 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:2217941 original size:4 final size:4
Alignment explanation
Indices: 2217932--2217956 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2217922 ATGATAGCAA
2217932 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2217957 TGCAAGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2219438 original size:29 final size:29
Alignment explanation
Indices: 2219406--2219466 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2219396 AATTATTAAT
*
2219406 TTTTAA-ATGATTAAATTA-AAATTTTATCA
1 TTTTAAGATG-TTAAAATATAAATTTTAT-A
*
2219435 TTTTAAGGTGTTAAAATATAAATTTTATA
1 TTTTAAGATGTTAAAATATAAATTTTATA
2219464 TTT
1 TTT
2219467 ATCAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (29 bp):
TTTTAAGATGTTAAAATATAAATTTTATA
Found at i:2220453 original size:8 final size:8
Alignment explanation
Indices: 2220440--2220513 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
2220430 TTATGTTTAG
2220440 TATATTAT
1 TATATTAT
2220448 TATATTAT
1 TATATTAT
2220456 TATATTAT
1 TATATTAT
*
2220464 TATATAAT
1 TATATTAT
* *
2220472 AAATATTTT
1 -TATATTAT
*
2220481 TATGTT-T
1 TATATTAT
2220488 TA-ATTATAT
1 TATA-T-TAT
2220497 TATATTAT
1 TATATTAT
2220505 ATATATTAT
1 -TATATTAT
2220514 ATAAACTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
7 4 0.08
8 31 0.58
9 17 0.32
10 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:2221806 original size:15 final size:15
Alignment explanation
Indices: 2221786--2221842 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
2221776 CGATGAATTT
*
2221786 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
2221801 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
2221816 ATTGAAATTATATTG
1 ATTGAAATTATATTG
2221831 ATTG-AATTATAT
1 ATTGAAATTATAT
2221843 AATATAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:2222255 original size:23 final size:23
Alignment explanation
Indices: 2222226--2222300 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 23
2222216 CGGTACTTTA
2222226 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
2222249 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* * **
2222270 TGTGTTGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
2222291 TGTGTCGTAT
1 TGTGTCGTAT
2222301 ACTGATTAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 33 0.75
22 2 0.05
23 9 0.20
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:2222330 original size:19 final size:19
Alignment explanation
Indices: 2222306--2222342 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2222296 CGTATACTGA
*
2222306 TTAGGCACTATGTACCGTT
1 TTAGGCACAATGTACCGTT
*
2222325 TTAGGCACAATGTGCCGT
1 TTAGGCACAATGTACCGT
2222343 ACTGGTGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (19 bp):
TTAGGCACAATGTACCGTT
Found at i:2224440 original size:35 final size:35
Alignment explanation
Indices: 2224401--2224497 Score: 167
Period size: 35 Copynumber: 2.8 Consensus size: 35
2224391 CATGGAAAAG
* *
2224401 TGTGAAATGTAGGTATGGTATCATCAATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCAATACTGAGC
*
2224436 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCAATACTGAGC
2224471 TGTGAAATGTAGGTATGGTATTATCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
2224498 ATCCATACTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCAATACTGAGC
Found at i:2224560 original size:35 final size:35
Alignment explanation
Indices: 2224405--2224570 Score: 156
Period size: 35 Copynumber: 4.6 Consensus size: 35
2224395 GAAAAGTGTG
* * **
2224405 AAATGTAGGTATGGTATCAT-CAATACTGAGTTGTG
1 AAATGTAGGTATGGTAT-TTCCCATACTGAGTTGAA
* **
2224440 AAATGTAGGTATGGTATTAT-CCATACTGAGCTGTG
1 AAATGTAGGTATGGTATT-TCCCATACTGAGTTGAA
*
2224475 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAA
1 AAATGTAGGTATGGTATT-TC----CCATACTGAGTT-GAA
* *
2224516 AAATGTAGGTATGGCATTTCCCATACCGAGTTGAA
1 AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
2224551 AAATGTAGGTATGGTATTTC
1 AAATGTAGGTATGGTATTTC
2224571 AATGAGGAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
35 72 0.64
36 11 0.10
40 13 0.12
41 17 0.15
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
Found at i:2235377 original size:25 final size:25
Alignment explanation
Indices: 2235348--2235400 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2235338 TATACGGTTA
2235348 CTTTCATGTGTTTAATTACTTATTT
1 CTTTCATGTGTTTAATTACTTATTT
2235373 CTTTCATGTGTTTAATTACTTATTT
1 CTTTCATGTGTTTAATTACTTATTT
2235398 CTT
1 CTT
2235401 ATTGAAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (25 bp):
CTTTCATGTGTTTAATTACTTATTT
Found at i:2240250 original size:34 final size:32
Alignment explanation
Indices: 2240208--2240270 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
2240198 AATTTGCTTT
*
2240208 TTTTTTTTGCTGTTTTCTTGGTATTTTTTTACTC
1 TTTTTTTTGCTATTTTCTT-GT-TTTTTTTACTC
2240242 TTTTTTTTGCTATTTTCTTGTTTTTTTTA
1 TTTTTTTTGCTATTTTCTTGTTTTTTTTA
2240271 TTATTTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 8 0.29
33 2 0.07
34 18 0.64
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.75
Consensus pattern (32 bp):
TTTTTTTTGCTATTTTCTTGTTTTTTTTACTC
Found at i:2242383 original size:53 final size:53
Alignment explanation
Indices: 2242242--2242392 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
2242232 ATAAGTGCGC
* **
2242242 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
2242295 CTGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
2242348 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
2242393 ACCGTGTAAG
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:2245392 original size:26 final size:26
Alignment explanation
Indices: 2245363--2245422 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
2245353 TCCCTTTGAA
* * *
2245363 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
2245389 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
2245417 CCATTC
1 TCATTC
2245423 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:2245408 original size:28 final size:28
Alignment explanation
Indices: 2245377--2245448 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2245367 TCGATATTTT
*
2245377 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
2245405 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
2245433 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
2245449 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:2262666 original size:4 final size:4
Alignment explanation
Indices: 2262648--2262680 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
2262638 TTGCATTGTA
2262648 GTTT GGTTT -TTT GTTT GTTT GTTT GTTT GTTT G
1 GTTT -GTTT GTTT GTTT GTTT GTTT GTTT GTTT G
2262681 GCTTTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (4 bp):
GTTT
Found at i:2266895 original size:25 final size:25
Alignment explanation
Indices: 2266875--2266921 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2266865 ATTAAATTAA
2266875 AAAAACAAAATAAT-TTTTAAAAAC
1 AAAAACAAAATAATATTTTAAAAAC
* *
2266899 TAAAATAAAATAATATTTTAAAA
1 AAAAACAAAATAATATTTTAAAA
2266922 TTTATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAAACAAAATAATATTTTAAAAAC
Found at i:2270188 original size:2 final size:2
Alignment explanation
Indices: 2270181--2270211 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2270171 AAGTTCTTAA
2270181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2270212 AACAGAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2274860 original size:31 final size:31
Alignment explanation
Indices: 2274825--2274884 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2274815 AAAAAAACTT
2274825 AATAGTCTAATGA-CTCAAATAAAAACTTTTG
1 AATAGTCTAAT-ATCTCAAATAAAAACTTTTG
* * *
2274856 AATAGTTTAATATCTTAAATGAAAACTTT
1 AATAGTCTAATATCTCAAATAAAAACTTT
2274885 CAATAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (31 bp):
AATAGTCTAATATCTCAAATAAAAACTTTTG
Found at i:2283083 original size:22 final size:22
Alignment explanation
Indices: 2283058--2283106 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2283048 TGTTTTCTCC
2283058 TTATTTTGCTACCATTTTATTA
1 TTATTTTGCTACCATTTTATTA
* * * *
2283080 TTATGTTGCTACTATTTTGTTG
1 TTATTTTGCTACCATTTTATTA
2283102 TTATT
1 TTATT
2283107 GTTTGGATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.61
Consensus pattern (22 bp):
TTATTTTGCTACCATTTTATTA
Found at i:2283304 original size:17 final size:17
Alignment explanation
Indices: 2283282--2283318 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2283272 GAAATATAAG
2283282 TTTACATATTTTTTAAA
1 TTTACATATTTTTTAAA
2283299 TTTACATATTTTTTAAA
1 TTTACATATTTTTTAAA
2283316 TTT
1 TTT
2283319 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTACATATTTTTTAAA
Found at i:2283304 original size:64 final size:64
Alignment explanation
Indices: 2283229--2283363 Score: 261
Period size: 64 Copynumber: 2.1 Consensus size: 64
2283219 TTTAGTGTTA
*
2283229 TTTAAGTTTACATATTTTTTAAATTTTATTTTTAATTTTTTGAGAAATATAAGTTTACATATTT
1 TTTAAATTTACATATTTTTTAAATTTTATTTTTAATTTTTTGAGAAATATAAGTTTACATATTT
2283293 TTTAAATTTACATATTTTTTAAATTTTATTTTTAATTTTTTGAGAAATATAAGTTTACATATTT
1 TTTAAATTTACATATTTTTTAAATTTTATTTTTAATTTTTTGAGAAATATAAGTTTACATATTT
2283357 TTTAAAT
1 TTTAAAT
2283364 ATCTATTTTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (64 bp):
TTTAAATTTACATATTTTTTAAATTTTATTTTTAATTTTTTGAGAAATATAAGTTTACATATTT
Found at i:2291440 original size:14 final size:14
Alignment explanation
Indices: 2291423--2291456 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2291413 ATAAATTTTA
*
2291423 AAATGAAAAAAATT
1 AAATGAAAAAAATC
2291437 AAATGAAAAAAATC
1 AAATGAAAAAAATC
2291451 AAATGA
1 AAATGA
2291457 TATAAGGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (14 bp):
AAATGAAAAAAATC
Found at i:2299854 original size:12 final size:12
Alignment explanation
Indices: 2299833--2299866 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2299823 TATATATTTT
*
2299833 AAAATTATATAA
1 AAAATAATATAA
2299845 AAAATAATATAA
1 AAAATAATATAA
*
2299857 AAATTAATAT
1 AAAATAATAT
2299867 GAGCGGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:2304428 original size:24 final size:25
Alignment explanation
Indices: 2304401--2304448 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2304391 TTATGAAGTT
**
2304401 TTTCT-CACCTTTTGGACCATTTTA
1 TTTCTCCACCTTAGGGACCATTTTA
*
2304425 TTTCTCCATCTTAGGGACCATTTT
1 TTTCTCCACCTTAGGGACCATTTT
2304449 TTGTTTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.17, C:0.25, G:0.10, T:0.48
Consensus pattern (25 bp):
TTTCTCCACCTTAGGGACCATTTTA
Found at i:2304545 original size:1 final size:1
Alignment explanation
Indices: 2304539--2304564 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2304529 CCTCTATACC
2304539 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
2304565 GCTGATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2310755 original size:94 final size:95
Alignment explanation
Indices: 2310610--2310794 Score: 318
Period size: 94 Copynumber: 2.0 Consensus size: 95
2310600 TCACAGTTAG
2310610 TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG
1 TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG
*
2310675 CTGCCCATCTCTTCGCTGTTGTATAGTTTT
66 CTGCACATCTCTTCGCTGTTGTATAGTTTT
* * *
2310705 TTTTTTTTTTTTTAATAATCTAAACTTCT-GACATCCCTTTTGTTGTAATGCCATTTACTGGCTG
1 TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG
*
2310769 CTGCACATCTCTTTGCTGTTGTATAG
66 CTGCACATCTCTTCGCTGTTGTATAG
2310795 AAATTAAACA
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
94 58 0.68
95 27 0.32
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.48
Consensus pattern (95 bp):
TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG
CTGCACATCTCTTCGCTGTTGTATAGTTTT
Found at i:2312132 original size:15 final size:16
Alignment explanation
Indices: 2312098--2312134 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2312088 AACAACCAGT
*
2312098 TCAA-ACAATGGGTCA
1 TCAATACAATGGGACA
2312113 TCAATACAATGGGACA
1 TCAATACAATGGGACA
2312129 -CAATAC
1 TCAATAC
2312135 GCTCCGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (16 bp):
TCAATACAATGGGACA
Found at i:2312355 original size:4 final size:4
Alignment explanation
Indices: 2312346--2312376 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2312336 ATGTAATAGC
2312346 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC
2312377 AAGTATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
ATCT
Found at i:2319449 original size:3 final size:3
Alignment explanation
Indices: 2319436--2319584 Score: 82
Period size: 3 Copynumber: 51.0 Consensus size: 3
2319426 TATTTTTAAA
*
2319436 TAT TGT TAT TAT TAT TA- TATT TAT TA- TAT TA- TATT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT
* * * * *
2319479 TAC TGT TAC TAT TAT T-T TAT ATATT TAT TAC CAT TATT TAT T-T T-T
1 TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT TA-T TAT TAT TAT
* * * * *
2319524 TAT TAT TAT TAA TAA CA- TAT TGT TAT TTT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2319570 TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT
2319585 CATGGTACCA
Statistics
Matches: 112, Mismatches: 21, Indels: 26
0.70 0.13 0.16
Matches are distributed among these distances:
2 17 0.15
3 83 0.74
4 11 0.10
5 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2319467 original size:14 final size:14
Alignment explanation
Indices: 2319441--2319480 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2319431 TTAAATATTG
2319441 TTATTATTATTATAT
1 TTATTA-TATTATAT
2319456 TTATTATATTATAT
1 TTATTATATTATAT
*
2319470 TTATTTTATTA
1 TTATTATATTA
2319481 CTGTTACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATATTATAT
Found at i:2319467 original size:20 final size:20
Alignment explanation
Indices: 2319442--2319532 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 20
2319432 TAAATATTGT
2319442 TATTATTATTATATTTATTA
1 TATTATTATTATATTTATTA
2319462 TATTA-TATT-TATTTTATTA
1 TATTATTATTATA-TTTATTA
* *
2319481 CTGTTACTATTAT-TTTA-TA
1 -TATTATTATTATATTTATTA
**
2319500 TATTTATTACCATTATTTATT-
1 TA-TTATTATTA-TATTTATTA
*
2319521 TTTTATTATTAT
1 TATTATTATTAT
2319533 TAATAACATA
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.05
19 20 0.36
20 21 0.38
21 9 0.16
22 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (20 bp):
TATTATTATTATATTTATTA
Found at i:2319750 original size:17 final size:17
Alignment explanation
Indices: 2319728--2319779 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
2319718 ATTTTTTCTC
2319728 TATATTATTATTATTTT
1 TATATTATTATTATTTT
2319745 TATATTATT-TTCATTTT
1 TATATTATTATT-ATTTT
2319762 TATTAATATATTATTATT
1 TA-T-AT-TATTATTATT
2319780 ATTGTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.07
17 16 0.53
18 1 0.03
19 2 0.07
20 7 0.23
21 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTATTATTATTTT
Found at i:2319993 original size:2 final size:2
Alignment explanation
Indices: 2319986--2320013 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2319976 CATCAACCTC
2319986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2320014 TATTTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2331535 original size:20 final size:21
Alignment explanation
Indices: 2331498--2331537 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2331488 TCTAATTAAG
2331498 AAAAAAGATAATAGCTAAAAT
1 AAAAAAGATAATAGCTAAAAT
* *
2331519 AAAAAA-ATCATATCTAAAA
1 AAAAAAGATAATAGCTAAAA
2331538 AAACTAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAAGATAATAGCTAAAAT
Found at i:2332229 original size:2 final size:2
Alignment explanation
Indices: 2332222--2332258 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2332212 AATGCAAATT
2332222 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
2332259 TTCTCCCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2332602 original size:4 final size:4
Alignment explanation
Indices: 2332593--2332620 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2332583 ACTACAAGTT
2332593 CAAA CAAA CAAA CAAA CAAA CAAA CAAA
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA
2332621 AAAAAAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:2337944 original size:25 final size:26
Alignment explanation
Indices: 2337897--2337945 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2337887 CATGTCATTT
**
2337897 ATTTTTTATATAATATTCTTATTAAG
1 ATTTTTTATATAATATTAATATTAAG
*
2337923 ATTTTTTTTA-AATATTAATATTA
1 ATTTTTTATATAATATTAATATTA
2337946 TTATAAGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTTTATATAATATTAATATTAAG
Found at i:2339814 original size:15 final size:15
Alignment explanation
Indices: 2339794--2339829 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2339784 TACTAACCAT
2339794 TAAGCATAACATATA
1 TAAGCATAACATATA
2339809 TAAGCATAACATATA
1 TAAGCATAACATATA
2339824 TAAGCA
1 TAAGCA
2339830 AGACAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (15 bp):
TAAGCATAACATATA
Found at i:2340496 original size:25 final size:25
Alignment explanation
Indices: 2340466--2340542 Score: 109
Period size: 25 Copynumber: 2.9 Consensus size: 25
2340456 AAAAAAAAAA
2340466 AAAAAAAAGAAAAAGAAAAACCTAACC
1 AAAAAAAA-AAAAA-AAAAACCTAACC
2340493 AAAAAAAAAAAAAAAAAACCTAACC
1 AAAAAAAAAAAAAAAAAACCTAACC
2340518 AAAAATAAATAAATAAAAAAACCTA
1 AAAAA-AAA-AAA-AAAAAAACCTA
2340543 GCCACCTAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
25 17 0.36
26 8 0.17
27 11 0.23
28 11 0.23
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.08
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAACCTAACC
Found at i:2340496 original size:28 final size:26
Alignment explanation
Indices: 2340465--2340542 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 26
2340455 AAAAAAAAAA
2340465 AAAAAAAAAGAAAAAGAAAAACCTAACC
1 AAAAAAAAA-AAAAA-AAAAACCTAACC
2340493 -AAAAAAAAAAAAAAAAAACCTAACC
1 AAAAAAAAAAAAAAAAAAACCTAACC
*
2340518 AAAAATAAATAAATAAAAAAACCTA
1 AAAAA-AAA-AAAAAAAAAAACCTA
2340543 GCCACCTAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
25 12 0.26
26 9 0.20
27 11 0.24
28 14 0.30
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.08
Consensus pattern (26 bp):
AAAAAAAAAAAAAAAAAAACCTAACC
Found at i:2340775 original size:18 final size:17
Alignment explanation
Indices: 2340736--2340774 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2340726 CCTAAAGGTG
*
2340736 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
2340753 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
2340770 ATTTT
1 ATTTT
2340775 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:2341318 original size:11 final size:11
Alignment explanation
Indices: 2341300--2341329 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2341290 GTGTATATTG
2341300 TATATATTATA
1 TATATATTATA
*
2341311 TTTATATTATA
1 TATATATTATA
2341322 TATATATT
1 TATATATT
2341330 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:2342810 original size:25 final size:25
Alignment explanation
Indices: 2342781--2342834 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
2342771 TATATATACC
*
2342781 ATAACACAACAAAATGCAAAATATT
1 ATAACACAACAAAAAGCAAAATATT
2342806 ATAACACAACAAAAAGCAAAATATT
1 ATAACACAACAAAAAGCAAAATATT
2342831 ATAA
1 ATAA
2342835 GATTTGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.63, C:0.15, G:0.04, T:0.19
Consensus pattern (25 bp):
ATAACACAACAAAAAGCAAAATATT
Found at i:2345306 original size:2 final size:2
Alignment explanation
Indices: 2345299--2345341 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2345289 TTATAACTTA
2345299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2345341 A
1 A
2345342 AAAGTTAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2349685 original size:13 final size:13
Alignment explanation
Indices: 2349667--2349693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2349657 ACTCCTGGTA
2349667 CAAAAGCCTCTAT
1 CAAAAGCCTCTAT
2349680 CAAAAGCCTCTAT
1 CAAAAGCCTCTAT
2349693 C
1 C
2349694 GTACTTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (13 bp):
CAAAAGCCTCTAT
Found at i:2351807 original size:26 final size:26
Alignment explanation
Indices: 2351771--2351821 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2351761 AGATCATGGG
2351771 AATTAGCCTCACATTGTAGACTAAGC
1 AATTAGCCTCACATTGTAGACTAAGC
2351797 AATTAGCCTCACATTGTAGACTAAG
1 AATTAGCCTCACATTGTAGACTAAG
2351822 TACTTCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (26 bp):
AATTAGCCTCACATTGTAGACTAAGC
Found at i:2359996 original size:18 final size:18
Alignment explanation
Indices: 2359952--2359985 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2359942 CAGTTTTGTT
2359952 TTTGTTTTTCAGTGCTTA
1 TTTGTTTTTCAGTGCTTA
*
2359970 TTTGATTTTCAG-GCTT
1 TTTGTTTTTCAGTGCTT
2359986 TGCTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (18 bp):
TTTGTTTTTCAGTGCTTA
Found at i:2361100 original size:19 final size:19
Alignment explanation
Indices: 2361078--2361116 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2361068 TTTTTAACAC
2361078 ATTAGAAATATATTAAAAA
1 ATTAGAAATATATTAAAAA
2361097 ATTAGAAATATATTAAAAA
1 ATTAGAAATATATTAAAAA
2361116 A
1 A
2361117 ACATTACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
ATTAGAAATATATTAAAAA
Found at i:2361340 original size:20 final size:20
Alignment explanation
Indices: 2361290--2361333 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2361280 TGGGTTAGTG
*
2361290 ATTATTAATATAA-ATATATA
1 ATTATT-ATTTAACATATATA
2361310 ATTATTATTTAACATATATA
1 ATTATTATTTAACATATATA
2361330 ATTA
1 ATTA
2361334 ATTTTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTATTATTTAACATATATA
Done.