Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 11 of 318
Found at i:3924368 original size:5 final size:5
Alignment explanation
Indices: 3924358--3924408 Score: 95
Period size: 5 Copynumber: 10.4 Consensus size: 5
3924348 TTATGTTTTA
3924358 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
3924407 AT
1 AT
3924409 AAACTAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:3924918 original size:23 final size:23
Alignment explanation
Indices: 3924892--3924950 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
3924882 GCACTTTATT
3924892 TGTCGTATTTTAGGCACCTCGTG
1 TGTCGTATTTTAGGCACCTCGTG
*
3924915 TGTCGTA--TCAGGCACCTCGTG
1 TGTCGTATTTTAGGCACCTCGTG
3924936 TGTCG--TTTTAGGCAC
1 TGTCGTATTTTAGGCAC
3924951 TTTATGTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 25 0.78
23 7 0.22
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.36
Consensus pattern (23 bp):
TGTCGTATTTTAGGCACCTCGTG
Found at i:3924958 original size:21 final size:21
Alignment explanation
Indices: 3924899--3924962 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3924889 ATTTGTCGTA
*
3924899 TTTTAGGCACCTCGTGTGTCG
1 TTTTAGGCACCTCATGTGTCG
* * *
3924920 TATCAGGCACCTCGTGTGTCG
1 TTTTAGGCACCTCATGTGTCG
* *
3924941 TTTTAGGCACTTTATGTGTCG
1 TTTTAGGCACCTCATGTGTCG
3924962 T
1 T
3924963 ACTCTAATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (21 bp):
TTTTAGGCACCTCATGTGTCG
Found at i:3925507 original size:2 final size:2
Alignment explanation
Indices: 3925500--3925577 Score: 52
Period size: 2 Copynumber: 43.5 Consensus size: 2
3925490 ATTCTAGTTA
*
3925500 AT AT AT AT AT AT -T AT AT AT AT GT A- AGT A- AT GAT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT
3925539 -T A- AT AT AT -T AT AT -T AT AT -T AT AT -T 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
3925575 AT A
1 AT A
3925578 ACAAAAGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
1 11 0.18
2 47 0.77
3 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3925518 original size:13 final size:13
Alignment explanation
Indices: 3925500--3925574 Score: 63
Period size: 13 Copynumber: 5.9 Consensus size: 13
3925490 ATTCTAGTTA
3925500 ATATATATATATT
1 ATATATATATATT
*
3925513 ATATATATGTA--
1 ATATATATATATT
3925524 AGTA-ATGAT-TATT
1 A-TATAT-ATATATT
3925537 AT-TA-ATATATT
1 ATATATATATATT
3925548 ATATTATATTATATT
1 ATA-TATA-TATATT
3925563 ATATATATATAT
1 ATATATATATAT
3925575 ATAACAAAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
10 2 0.04
11 11 0.22
12 6 0.12
13 18 0.35
14 5 0.10
15 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (13 bp):
ATATATATATATT
Found at i:3925552 original size:5 final size:5
Alignment explanation
Indices: 3925542--3925576 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
3925532 TTATTATTAA
3925542 TATAT TATAT TATAT TATAT TATA- TATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
3925577 AACAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:3925868 original size:13 final size:13
Alignment explanation
Indices: 3925850--3925876 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3925840 TTTCCAGCAA
3925850 TTATGAATTTATT
1 TTATGAATTTATT
3925863 TTATGAATTTATT
1 TTATGAATTTATT
3925876 T
1 T
3925877 GATAATGATC
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:3926089 original size:50 final size:50
Alignment explanation
Indices: 3925976--3926217 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
3925966 ATTTGGGTAA
* * *
3925976 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
3926032 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3926082 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3926132 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
3926182 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
3926218 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:3926165 original size:100 final size:103
Alignment explanation
Indices: 3925976--3926225 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
3925966 ATTTGGGTAA
3925976 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
3926041 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
3926082 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
3926144 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
3926182 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
3926226 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:3928154 original size:5 final size:5
Alignment explanation
Indices: 3928144--3928179 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
3928134 TTATGTTTTA
3928144 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
3928180 AAACTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:3928689 original size:23 final size:23
Alignment explanation
Indices: 3928663--3928721 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
3928653 GCACTTTATT
3928663 TGTCGTATTTTAGGCACCTCGTG
1 TGTCGTATTTTAGGCACCTCGTG
*
3928686 TGTCGTA--TCAGGCACCTCGTG
1 TGTCGTATTTTAGGCACCTCGTG
3928707 TGTCG--TTTTAGGCAC
1 TGTCGTATTTTAGGCAC
3928722 TTTACGTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 25 0.78
23 7 0.22
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.36
Consensus pattern (23 bp):
TGTCGTATTTTAGGCACCTCGTG
Found at i:3957060 original size:12 final size:12
Alignment explanation
Indices: 3957043--3957068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3957033 AGACATGTAA
3957043 GTTTACTAATGG
1 GTTTACTAATGG
3957055 GTTTACTAATGG
1 GTTTACTAATGG
3957067 GT
1 GT
3957069 CTTTTCTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (12 bp):
GTTTACTAATGG
Found at i:3965251 original size:4 final size:4
Alignment explanation
Indices: 3965242--3965270 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3965232 CAATAGAGAT
3965242 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
3965271 GGAGGAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3970288 original size:29 final size:29
Alignment explanation
Indices: 3970246--3970303 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3970236 CTGTCAGCAG
3970246 ATAGTCAGGTTTGAGACTTATCTATCATT
1 ATAGTCAGGTTTGAGACTTATCTATCATT
3970275 ATAGTCAGGTTTGAGACTTATCTATCATT
1 ATAGTCAGGTTTGAGACTTATCTATCATT
3970304 CACATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (29 bp):
ATAGTCAGGTTTGAGACTTATCTATCATT
Found at i:3971920 original size:21 final size:21
Alignment explanation
Indices: 3971896--3971935 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3971886 TCTCCATCTC
* *
3971896 CACCTCCACCACGGCCACCCT
1 CACCCCCACCACCGCCACCCT
*
3971917 CACCCCCACCCCCGCCACC
1 CACCCCCACCACCGCCACC
3971936 ACCAGCACCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.70, G:0.07, T:0.05
Consensus pattern (21 bp):
CACCCCCACCACCGCCACCCT
Found at i:3977045 original size:11 final size:11
Alignment explanation
Indices: 3977029--3977076 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
3977019 TATACTCATC
3977029 CCTTGCCCATA
1 CCTTGCCCATA
3977040 CCTTGCCCATA
1 CCTTGCCCATA
*
3977051 CCTTTCCCATA
1 CCTTGCCCATA
*
3977062 CC-TACCCATA
1 CCTTGCCCATA
3977072 CCTTG
1 CCTTG
3977077 GAAAGGTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.19, C:0.46, G:0.06, T:0.29
Consensus pattern (11 bp):
CCTTGCCCATA
Found at i:3977638 original size:18 final size:18
Alignment explanation
Indices: 3977614--3977702 Score: 133
Period size: 18 Copynumber: 4.9 Consensus size: 18
3977604 ATCGTTTATA
3977614 GTACTATTCACGTATACG
1 GTACTATTCACGTATACG
* *
3977632 ATACTATTTACGTATACG
1 GTACTATTCACGTATACG
3977650 GTACTATTCACGTATACG
1 GTACTATTCACGTATACG
* *
3977668 GCACTGTTCACGTATACG
1 GTACTATTCACGTATACG
*
3977686 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
3977703 AGTAGTTGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (18 bp):
GTACTATTCACGTATACG
Found at i:3978560 original size:11 final size:11
Alignment explanation
Indices: 3978544--3978572 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3978534 TTAACTTGGT
3978544 TGGCATGGCAA
1 TGGCATGGCAA
3978555 TGGCATGGCAA
1 TGGCATGGCAA
3978566 TGGCATG
1 TGGCATG
3978573 TCAAACGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (11 bp):
TGGCATGGCAA
Found at i:3983954 original size:39 final size:39
Alignment explanation
Indices: 3983900--3984023 Score: 230
Period size: 39 Copynumber: 3.2 Consensus size: 39
3983890 CAAAATCTAG
*
3983900 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
*
3983939 CTGAAGCATATAAGTGCTAAACTGAAGCCCGAAGGCTAA
1 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
3983978 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
3984017 CTGAAGC
1 CTGAAGC
3984024 TCATCAGAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (39 bp):
CTGAAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAA
Found at i:3983962 original size:21 final size:21
Alignment explanation
Indices: 3983900--3984005 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
3983890 CAAAATCTAG
3983900 CTGAAGCACATAAGTGCTAAA
1 CTGAAGCACATAAGTGCTAAA
* **
3983921 CGGAAGC-CCGAAG-GCT-AA
1 CTGAAGCACATAAGTGCTAAA
*
3983939 CTGAAGCATATAAGTGCTAAA
1 CTGAAGCACATAAGTGCTAAA
**
3983960 CTGAAGC-CCGAAG-GCT-AA
1 CTGAAGCACATAAGTGCTAAA
*
3983978 CTGAAGCATATAAGTGCTAAA
1 CTGAAGCACATAAGTGCTAAA
*
3983999 CGGAAGC
1 CTGAAGC
3984006 CCGAAGGCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
18 17 0.26
19 12 0.18
20 13 0.20
21 23 0.35
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (21 bp):
CTGAAGCACATAAGTGCTAAA
Found at i:3983981 original size:18 final size:18
Alignment explanation
Indices: 3983923--3984023 Score: 85
Period size: 18 Copynumber: 5.3 Consensus size: 18
3983913 GTGCTAAACG
3983923 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
***
3983941 GAAGCATATAAGTGCTAAACT
1 GAAGC-CCGAAG-GCT-AACT
3983962 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
*** *
3983980 GAAGCATATAAGTGCTAAACG
1 GAAGC-CCGAAG-GCT-AACT
3984001 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
3984019 GAAGC
1 GAAGC
3984024 TCATCAGAGC
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
18 22 0.35
19 12 0.19
20 12 0.19
21 17 0.27
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (18 bp):
GAAGCCCGAAGGCTAACT
Found at i:3985466 original size:16 final size:16
Alignment explanation
Indices: 3985445--3985477 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3985435 ATGTATATAA
3985445 ACTTTCAATTTCTTTC
1 ACTTTCAATTTCTTTC
3985461 ACTTTCAATTTCTTTC
1 ACTTTCAATTTCTTTC
3985477 A
1 A
3985478 TAGAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (16 bp):
ACTTTCAATTTCTTTC
Found at i:3990194 original size:2 final size:2
Alignment explanation
Indices: 3990187--3990212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3990177 GAGAAAAAGT
3990187 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3990213 AGTGGATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3995724 original size:18 final size:20
Alignment explanation
Indices: 3995698--3995739 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
3995688 ATTTCATGTT
*
3995698 ATTTTAAAG-AAAGCCAA-A
1 ATTTAAAAGTAAAGCCAATA
*
3995716 ATTTAAAAGTAAAGTCAATA
1 ATTTAAAAGTAAAGCCAATA
3995736 ATTT
1 ATTT
3995740 TTAAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 7 0.35
20 5 0.25
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTTAAAAGTAAAGCCAATA
Found at i:4001219 original size:23 final size:23
Alignment explanation
Indices: 4001193--4001248 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
4001183 CTTTAGCACC
4001193 CGGGCGTGTGTTCTATACCTACA
1 CGGGCGTGTGTTCTATACCTACA
4001216 CGGGCGTGTGTTCTATACCTACA
1 CGGGCGTGTGTTCTATACCTACA
4001239 CGGGCGTGTG
1 CGGGCGTGTG
4001249 GAGCCTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.29
Consensus pattern (23 bp):
CGGGCGTGTGTTCTATACCTACA
Found at i:4002206 original size:18 final size:17
Alignment explanation
Indices: 4002185--4002228 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4002175 TTAATTTTTT
4002185 AAAATTATATAATATATA
1 AAAATTATATAATATA-A
*
4002203 AAAATAATATAATATAA
1 AAAATTATATAATATAA
*
4002220 AATATTATA
1 AAAATTATA
4002229 AACTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTATATAATATAA
Found at i:4015563 original size:42 final size:42
Alignment explanation
Indices: 4015504--4015588 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
4015494 GGAATGGCCA
*
4015504 TAATTATAAAGTTTGGTGGGACAACTATCTTATAGATTTGAT
1 TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
*
4015546 TAATTATAAAGTTTGGTGGGACAAGTATCTTACAGATTTGAT
1 TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
4015588 T
1 T
4015589 TAATAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (42 bp):
TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
Found at i:4017865 original size:31 final size:33
Alignment explanation
Indices: 4017830--4017901 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
4017820 ATATCCAAAA
*
4017830 TCAAAATAACT-TGAATAAAAAAT-ACTTAAAT-
1 TCAAAATAA-TATAAATAAAAAATGACTTAAATC
**
4017861 TCAAAATAATATAAATCTAAAATGACTTAAATC
1 TCAAAATAATATAAATAAAAAATGACTTAAATC
4017894 TCAAAATA
1 TCAAAATA
4017902 GAAATGATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 18 0.51
32 8 0.23
33 8 0.23
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (33 bp):
TCAAAATAATATAAATAAAAAATGACTTAAATC
Found at i:4017912 original size:33 final size:31
Alignment explanation
Indices: 4017848--4017916 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
4017838 ACTTGAATAA
*
4017848 AAAATACTTAAATTCAAAATAATATAAATCT
1 AAAATACTTAAATTCAAAATAAAATAAATCT
*
4017879 AAAATGACTTAAATCTCAAAATAGAAAT-GATCT
1 AAAAT-ACTTAAAT-TCAAAATA-AAATAAATCT
4017912 AAAAT
1 AAAAT
4017917 CAATCTAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.15
32 8 0.24
33 17 0.52
34 3 0.09
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (31 bp):
AAAATACTTAAATTCAAAATAAAATAAATCT
Found at i:4018007 original size:23 final size:23
Alignment explanation
Indices: 4017981--4018025 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4017971 AACTCAAATT
*
4017981 TTTTAAAATAAAGTTGTGGATTC
1 TTTTAAAATAAAATTGTGGATTC
* *
4018004 TTTTAAAGTAAAATTTTGGATT
1 TTTTAAAATAAAATTGTGGATT
4018026 TAAATTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TTTTAAAATAAAATTGTGGATTC
Found at i:4024589 original size:14 final size:14
Alignment explanation
Indices: 4024570--4024597 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4024560 CTGCTTTCTA
4024570 AATTTGTTTTAAGG
1 AATTTGTTTTAAGG
4024584 AATTTGTTTTAAGG
1 AATTTGTTTTAAGG
4024598 CTGACAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
AATTTGTTTTAAGG
Found at i:4031591 original size:18 final size:19
Alignment explanation
Indices: 4031552--4031603 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
4031542 TTTATTTATA
4031552 ATTACAAATTAAA-TACATT
1 ATTA-AAATTAAATTACATT
*
4031571 ATTAAAATTAAATTAGA-T
1 ATTAAAATTAAATTACATT
4031589 ATTTAAAATATAAAT
1 A-TTAAAAT-TAAAT
4031604 AACAGTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTAAAATTAAATTACATT
Found at i:4031780 original size:12 final size:12
Alignment explanation
Indices: 4031742--4031781 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4031732 ATATTATTTT
*
4031742 TTATTTTAAAAA
1 TTATTTTAAATA
4031754 TTATTTTAAAGTA
1 TTATTTTAAA-TA
*
4031767 TTTTTTTAAATA
1 TTATTTTAAATA
4031779 TTA
1 TTA
4031782 AATTTATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TTATTTTAAATA
Found at i:4032263 original size:19 final size:20
Alignment explanation
Indices: 4032238--4032281 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4032228 TAGATTTCAA
4032238 AATAATTTATTA-GT-ATATT
1 AATAA-TTATTATGTGATATT
*
4032257 TATAATTATTATGTGATATT
1 AATAATTATTATGTGATATT
4032277 AATAA
1 AATAA
4032282 AAATTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
AATAATTATTATGTGATATT
Found at i:4032762 original size:22 final size:22
Alignment explanation
Indices: 4032720--4032761 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4032710 ATGTTTAGCT
*
4032720 GAAAATTATAAAAATAGTTTTA
1 GAAAATTAAAAAAATAGTTTTA
*
4032742 GAAAA-TAAAAAAATATTTTT
1 GAAAATTAAAAAAATAGTTTT
4032762 TTAAATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
GAAAATTAAAAAAATAGTTTTA
Found at i:4035174 original size:3 final size:3
Alignment explanation
Indices: 4035166--4035196 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
4035156 CGACAAACAC
4035166 CTT CTT CTT CTT CTT CTT CTT CTT CTCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT
4035197 TTCCTTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:4036394 original size:6 final size:6
Alignment explanation
Indices: 4036383--4036409 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4036373 AGTTGAAAGG
4036383 TGATGC TGATGC TGATGC TGATGC TGA
1 TGATGC TGATGC TGATGC TGATGC TGA
4036410 CGCCATTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (6 bp):
TGATGC
Found at i:4044714 original size:17 final size:17
Alignment explanation
Indices: 4044691--4044730 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4044681 TCGTTTGAAA
*
4044691 TAATTTAAT-TTTTTTT
1 TAATTTTATGTTTTTTT
*
4044707 TTATTTTATGTTTTTTT
1 TAATTTTATGTTTTTTT
4044724 TAATTTT
1 TAATTTT
4044731 TTTCTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TAATTTTATGTTTTTTT
Found at i:4065846 original size:21 final size:22
Alignment explanation
Indices: 4065806--4065846 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4065796 AATATTTAAA
*
4065806 TTTTATTAAAAATTAGAAAATC
1 TTTTATTAAAAATCAGAAAATC
*
4065828 TTTTA-TAAAAATCATAAAA
1 TTTTATTAAAAATCAGAAAA
4065847 AAATTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTTATTAAAAATCAGAAAATC
Found at i:4065925 original size:21 final size:22
Alignment explanation
Indices: 4065884--4065957 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 22
4065874 AATAAATTAT
* * *
4065884 AAAATTTTATAAAGTCG-AAAG
1 AAAATTATAAAAAATCGTAAAG
4065905 AAAATTATAAAAAAT-GTAAAG
1 AAAATTATAAAAAATCGTAAAG
* *
4065926 -AAA-TAT-AAAATTCGTAAAA
1 AAAATTATAAAAAATCGTAAAG
4065945 AAAATTATAAAAA
1 AAAATTATAAAAA
4065958 TTATCATACT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 5 0.12
19 8 0.19
20 7 0.16
21 19 0.44
22 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (22 bp):
AAAATTATAAAAAATCGTAAAG
Found at i:4088002 original size:31 final size:31
Alignment explanation
Indices: 4087967--4088032 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4087957 AATTTGTCAC
* *
4087967 TATTTAAAATTTTTTATTTAAGTCATTGAAT
1 TATTTAAAAGTTTTTATTCAAGTCATTGAAT
* * * *
4087998 TATTTGAAAGTTTTTGTTCAAGTTATTGGAT
1 TATTTAAAAGTTTTTATTCAAGTCATTGAAT
4088029 TATT
1 TATT
4088033 AAGTCTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (31 bp):
TATTTAAAAGTTTTTATTCAAGTCATTGAAT
Found at i:4108488 original size:22 final size:22
Alignment explanation
Indices: 4108462--4108507 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4108452 ATGCAAGTCG
4108462 TTGAATAATTTAAAAATTTTCA
1 TTGAATAATTTAAAAATTTTCA
* *
4108484 TTGAATAGTTTAAAAGTTTTCA
1 TTGAATAATTTAAAAATTTTCA
4108506 TT
1 TT
4108508 TAAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (22 bp):
TTGAATAATTTAAAAATTTTCA
Found at i:4120668 original size:23 final size:23
Alignment explanation
Indices: 4120637--4120735 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
4120627 AGTGTTATTG
* *
4120637 ATCAGTGGTAGCTTCGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4120660 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
4120683 AACAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4120706 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4120729 ATCAGTG
1 ATCAGTG
4120736 TTGCACTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4124530 original size:12 final size:12
Alignment explanation
Indices: 4124515--4124545 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4124505 TTCTCTTTTA
4124515 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
4124527 TTTTTCTTTCTC
1 TTTTTCTTTCCC
4124539 TTTTTCT
1 TTTTTCT
4124546 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:4124646 original size:16 final size:16
Alignment explanation
Indices: 4124625--4124655 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4124615 TTTATTATTT
4124625 TATTAACATAATATAA
1 TATTAACATAATATAA
*
4124641 TATTAATATAATATA
1 TATTAACATAATATA
4124656 TTAAAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:4126552 original size:18 final size:19
Alignment explanation
Indices: 4126529--4126566 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4126519 TTTAAACTAA
*
4126529 ATTTAACTCCCT-AATTTC
1 ATTTAAATCCCTAAATTTC
4126547 ATTTAAATCCCTAAATTTC
1 ATTTAAATCCCTAAATTTC
4126566 A
1 A
4126567 AATTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAATCCCTAAATTTC
Found at i:4127475 original size:24 final size:24
Alignment explanation
Indices: 4127448--4127509 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
4127438 TAGCTCTTCG
*
4127448 GAGCTACCCGTTATTGGCTCGTAT
1 GAGCTTCCCGTTATTGGCTCGTAT
* *
4127472 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGTAT
4127496 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
4127510 ATAGCCCGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.09
24 26 0.81
25 3 0.09
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGTAT
Found at i:4127526 original size:49 final size:49
Alignment explanation
Indices: 4127423--4127527 Score: 113
Period size: 48 Copynumber: 2.1 Consensus size: 49
4127413 TGACTATCCA
* * * *
4127423 AAGCTTCCTGAATAATAGCTCTTCGGAGCTACCCGTTATTGGCTCGTAT
1 AAGCTTCCTGAATAATAGCTCTTAGGAGCTACCCGTTATTAGCCCGGAT
* * * * *
4127472 GAGCTTCCTG-ATTATGGCTCTTATGAGCTTCCCGTTATATAGCCCGGAT
1 AAGCTTCCTGAATAATAGCTCTTAGGAGCTACCCGTTAT-TAGCCCGGAT
4127521 AAGCTTC
1 AAGCTTC
4127528 TCGTTATATG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
48 23 0.51
49 22 0.49
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (49 bp):
AAGCTTCCTGAATAATAGCTCTTAGGAGCTACCCGTTATTAGCCCGGAT
Found at i:4130077 original size:50 final size:50
Alignment explanation
Indices: 4130002--4130328 Score: 546
Period size: 50 Copynumber: 6.5 Consensus size: 50
4129992 CCATGGCAAC
* * *
4130002 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
4130052 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
4130102 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
4130152 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
4130202 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
4130252 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
4130303 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
4130329 CTGATCAATG
Statistics
Matches: 261, Mismatches: 15, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
50 238 0.91
51 23 0.09
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:4130346 original size:31 final size:31
Alignment explanation
Indices: 4130308--4130366 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
4130298 ATGGCAAGTA
4130308 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4130339 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
4130367 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:4130374 original size:46 final size:46
Alignment explanation
Indices: 4130321--4130412 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
4130311 AGTGGTAGCT
* *
4130321 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
4130367 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
4130413 GTGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:4130416 original size:31 final size:31
Alignment explanation
Indices: 4130368--4130436 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4130358 ACCTGATCAT
* * *
4130368 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
4130399 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
4130430 CGGCTAC
1 CGGCTAC
4130437 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:4135319 original size:50 final size:50
Alignment explanation
Indices: 4135243--4135518 Score: 444
Period size: 50 Copynumber: 5.5 Consensus size: 50
4135233 CCATGGCAAC
* *
4135243 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
4135293 AAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
4135343 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
4135393 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
4135443 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
4135494 AAGTAAAAAGTGGTAGCTTCGGCTA
1 AAGTGATAAGTGATAGCTTCGGCTA
4135519 TCTGATCAAT
Statistics
Matches: 209, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
50 187 0.89
51 22 0.11
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:4135539 original size:31 final size:32
Alignment explanation
Indices: 4135498--4135557 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
4135488 AATGGCAAGT
*
4135498 AAAAAGTGGTAGCTTCGGCTATCTGATCAATG
1 AAAAAGTGGTAGCTTCGGCTACCTGATCAATG
4135530 AAAAA-TGGTAGCTTCGGCTACCTGATCA
1 AAAAAGTGGTAGCTTCGGCTACCTGATCA
4135558 TCGGCTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (32 bp):
AAAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:4142853 original size:55 final size:53
Alignment explanation
Indices: 4142663--4142917 Score: 236
Period size: 55 Copynumber: 4.8 Consensus size: 53
4142653 ACGCGGGTAC
* * * *
4142663 CTTACCATTGCCATGACTTGTCATGGTCTTACATGGT-A---T-CCTTTTGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG-AA
* *
4142712 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATGAA
* * * *
4142765 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGG-AACATTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAAC-CTTGCCTTAT-G-AA
* * **
4142820 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG-AA
* * * *
4142873 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGTAACCTT
4142918 AAACCCTAAT
Statistics
Matches: 170, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
49 35 0.21
52 2 0.01
53 47 0.28
54 14 0.08
55 71 0.42
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATGAA
Found at i:4142854 original size:108 final size:110
Alignment explanation
Indices: 4142710--4142910 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
4142700 ATCCTTTTGA
* *
4142710 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
4142773 -TGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
* * *
4142818 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
4142883 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
4142911 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 27 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
Found at i:4145787 original size:30 final size:31
Alignment explanation
Indices: 4145753--4145821 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
4145743 TGGCCCAAGA
* * *
4145753 GTAAATATTCAAAATTTGAAGGATTAA-AGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
4145783 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
*
4145813 GAAAATATT
1 GTAAATATT
4145822 TTAAGGGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.48
30 16 0.48
31 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.30
Consensus pattern (31 bp):
GTAAATATTAAAAAGTTGAAGGACTAATAGT
Found at i:4145800 original size:29 final size:30
Alignment explanation
Indices: 4145753--4145820 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
4145743 TGGCCCAAGA
* * *
4145753 GTAAATATTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
4145783 GTAAATATAAAAAGTTGAAGGACTAATAGT
1 GTAAATATAAAAAGTTGAAGGACTAATAGT
*
4145813 GAAAATAT
1 GTAAATAT
4145821 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAGT
Found at i:4148016 original size:46 final size:46
Alignment explanation
Indices: 4147964--4148191 Score: 323
Period size: 46 Copynumber: 5.0 Consensus size: 46
4147954 AGTGTGCTCT
*
4147964 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
4148010 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAT
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4148056 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4148102 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
4148148 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
4148192 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:4148498 original size:16 final size:17
Alignment explanation
Indices: 4148477--4148509 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4148467 ATGATGGAGC
4148477 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
4148493 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
4148510 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:4150681 original size:63 final size:63
Alignment explanation
Indices: 4150603--4150728 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
4150593 TAAAATTTGA
4150603 GATGAAATGATAGAGAATGGATATAAATGATAAACTAGGTAAATATGTGCAAAAAGAAACTAT
1 GATGAAATGATAGAGAATGGATATAAATGATAAACTAGGTAAATATGTGCAAAAAGAAACTAT
4150666 GATGAAATGATAGAGAATGGATATAAATGATAAACTAGGTAAATATGTGCAAAAAGAAACTAT
1 GATGAAATGATAGAGAATGGATATAAATGATAAACTAGGTAAATATGTGCAAAAAGAAACTAT
4150729 AAAATTATAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.24
Consensus pattern (63 bp):
GATGAAATGATAGAGAATGGATATAAATGATAAACTAGGTAAATATGTGCAAAAAGAAACTAT
Found at i:4151020 original size:30 final size:31
Alignment explanation
Indices: 4150986--4151052 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
4150976 TGGCCCAAGA
* *
4150986 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATACTCAAAAGTTGAAGGACTAATAGT
* *
4151016 GTAAAT-GTGAAAAGTTGAAGGACTAATAGT
1 GTAAATACTCAAAAGTTGAAGGACTAATAGT
*
4151046 GCAAATA
1 GTAAATA
4151053 TTTTAAGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAAATACTCAAAAGTTGAAGGACTAATAGT
Found at i:4156081 original size:28 final size:28
Alignment explanation
Indices: 4156028--4156111 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
4156018 CACTTTGTGC
4156028 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
4156057 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
4156085 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
4156112 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:4156123 original size:23 final size:24
Alignment explanation
Indices: 4156032--4156125 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
4156022 TTGTGCTATT
4156032 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
4156059 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
4156089 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
4156112 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
4156126 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:4156353 original size:22 final size:23
Alignment explanation
Indices: 4156316--4156360 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
4156306 GCTTTACTGA
4156316 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
4156339 TCAGGCAC-TTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
4156361 CTGATTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:4157097 original size:42 final size:42
Alignment explanation
Indices: 4157050--4157134 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
4157040 TATGATATTA
*
4157050 TGTGTCTGACTTGTTTGGTTAAGTAAATGCTATGAGTAAATT
1 TGTGTCTGACTTGTTTGGTTAAGTAAATGCTATGAGCAAATT
4157092 TGTGTCTGACTTGTTTGGTTAAGTAAATGCTATGAGCAAATT
1 TGTGTCTGACTTGTTTGGTTAAGTAAATGCTATGAGCAAATT
4157134 T
1 T
4157135 ACTCAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (42 bp):
TGTGTCTGACTTGTTTGGTTAAGTAAATGCTATGAGCAAATT
Found at i:4160928 original size:46 final size:46
Alignment explanation
Indices: 4160861--4161133 Score: 388
Period size: 46 Copynumber: 5.9 Consensus size: 46
4160851 GTGTGCTCTC
**
4160861 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
** *
4160907 TGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* *
4160953 TTATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* *
4160999 TGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
*
4161045 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* * * *
4161091 TGACA-GAAAAT-AAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGATATG-AAATGAA-TAAGACCATGGTTGAAAGATACCATGGCA
4161134 TCATGTCAAA
Statistics
Matches: 208, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 3 0.01
46 205 0.99
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:4165464 original size:4 final size:4
Alignment explanation
Indices: 4165455--4165533 Score: 52
Period size: 4 Copynumber: 19.2 Consensus size: 4
4165445 CCCTTTTTTA
* ** * **
4165455 TTTC TTTC TTTC TTTC CTTC TTTC TTTC TCAC GTTTGC TCTC TGTT- AGTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC T-TTC TTTC
* *
4165505 TTTC TATA TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
4165534 CACGTTTGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
3 1 0.02
4 49 0.89
5 4 0.07
6 1 0.02
ACGTcount: A:0.05, C:0.25, G:0.05, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:4165577 original size:14 final size:14
Alignment explanation
Indices: 4165558--4165588 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4165548 GTAACTTTTC
4165558 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
4165572 TATTCTTTATTCAT
1 TATTCTTTACTCAT
4165586 TAT
1 TAT
4165589 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:4166222 original size:16 final size:17
Alignment explanation
Indices: 4166201--4166233 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4166191 ATGATGGAGC
4166201 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
4166217 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
4166234 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:4167060 original size:165 final size:167
Alignment explanation
Indices: 4166803--4167120 Score: 577
Period size: 165 Copynumber: 1.9 Consensus size: 167
4166793 TTAAATTTAA
*
4166803 ATTATATATTTTTAAAAATATTTATGTATTTTTATTTTTTTTTTGAATTTTTTAGATTTAGAATC
1 ATTATATATTTTTAAAAATATTTATGTATTTTTATTATTTTTTTGAATTTTTTAGATTTAGAATC
* *
4166868 AAATTGAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTT
66 AAATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTA
* *
4166933 TATAAAAGTTGAA-TTTAAATTTAAATTTAAATTATT
131 TATAAAAGGTGAAGGTTAAATTTAAATTTAAATTATT
4166969 ATTATATATTTTTAAAAATATTTATGTATTTTTA-TATTTTTTTGAATTTTTTAGATTTAGAATC
1 ATTATATATTTTTAAAAATATTTATGTATTTTTATTATTTTTTTGAATTTTTTAGATTTAGAATC
4167033 AAATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTA
66 AAATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTA
4167098 TATAAAAGGTGAAGGTTAAATTT
131 TATAAAAGGTGAAGGTTAAATTT
4167121 GTTATTATAC
Statistics
Matches: 146, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
165 104 0.71
166 42 0.29
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (167 bp):
ATTATATATTTTTAAAAATATTTATGTATTTTTATTATTTTTTTGAATTTTTTAGATTTAGAATC
AAATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTA
TATAAAAGGTGAAGGTTAAATTTAAATTTAAATTATT
Found at i:4180668 original size:17 final size:19
Alignment explanation
Indices: 4180632--4180669 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
4180622 TCTTAACAAT
*
4180632 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTCTAA
4180651 AATTC-AAAT-ATTTCTAA
1 AATTCAAAATAATTTCTAA
4180668 AA
1 AA
4180670 ATTCCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATAATTTCTAA
Found at i:4180750 original size:40 final size:41
Alignment explanation
Indices: 4180692--4180770 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
4180682 ATATTTTTAA
*
4180692 AATATATATAAAAATTAAATATTCTAAAA-AAAATCTAATG
1 AATATATATAAAAATTAAAAATTCTAAAAGAAAATCTAATG
* *
4180732 AATATATA-AAAAAGTTAAAAATTTTAAAAGAAATTCTAA
1 AATATATATAAAAA-TTAAAAATTCTAAAAGAAAATCTAA
4180771 AGTAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 5 0.15
40 21 0.62
41 8 0.24
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (41 bp):
AATATATATAAAAATTAAAAATTCTAAAAGAAAATCTAATG
Found at i:4184707 original size:3 final size:3
Alignment explanation
Indices: 4184701--4184729 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4184691 AAAAAGGAAA
4184701 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4184730 GAAGGAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4188524 original size:129 final size:129
Alignment explanation
Indices: 4188294--4188554 Score: 522
Period size: 129 Copynumber: 2.0 Consensus size: 129
4188284 TGTTCACTTT
4188294 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
1 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
4188359 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
66 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
4188423 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
1 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
4188488 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
66 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
4188552 AAT
1 AAT
4188555 GGTAAAATAC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 132 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (129 bp):
AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
Found at i:4191079 original size:15 final size:15
Alignment explanation
Indices: 4191059--4191088 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4191049 ATGGATTCAT
*
4191059 TAAAAAGTAAATAAA
1 TAAAAAATAAATAAA
4191074 TAAAAAATAAATAAA
1 TAAAAAATAAATAAA
4191089 AGAGGGGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAATAAA
Found at i:4191467 original size:64 final size:66
Alignment explanation
Indices: 4191363--4191494 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 66
4191353 TCCACGATGG
*
4191363 AACAGGAAAAAAATGGATGACACCCATTCTTGATTACAATGTTC-TTTAAGGATAATTCGACAAA
1 AACAGGAAAAAAATGGATGACACCCATTCTAGATTACAATGTTCTTTTAAGGATAATTCGACAAA
4191427 C
66 C
*
4191428 AACAGG-AAAAAAT-GATTGACACCCATTCTAGATTGCAATGTTCTTTTAAGGATAATTCGACAA
1 AACAGGAAAAAAATGGA-TGACACCCATTCTAGATTACAATGTTCTTTTAAGGATAATTCGACAA
4191491 AC
65 AC
4191493 AA
1 AA
4191495 GGAGGAAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
63 2 0.03
64 32 0.51
65 29 0.46
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (66 bp):
AACAGGAAAAAAATGGATGACACCCATTCTAGATTACAATGTTCTTTTAAGGATAATTCGACAAA
C
Found at i:4193124 original size:46 final size:46
Alignment explanation
Indices: 4193071--4193185 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
4193061 GACGGTTTGG
* *
4193071 CTCGAATTATTTATTTAAATTAATCTATAAATTTAATCCGGATTGA
1 CTCGAATTATTTATTTAAATTAATCTATAAACTTAATCCAGATTGA
* * * *
4193117 CTCGAATTATTTACTTAAACTAATCTATAAACTTAATTCAGTTTGA
1 CTCGAATTATTTATTTAAATTAATCTATAAACTTAATCCAGATTGA
4193163 CTCGAATTATTTATTTAAATTAA
1 CTCGAATTATTTATTTAAATTAA
4193186 CCGTTGAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (46 bp):
CTCGAATTATTTATTTAAATTAATCTATAAACTTAATCCAGATTGA
Found at i:4196772 original size:16 final size:16
Alignment explanation
Indices: 4196753--4196797 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
4196743 CAAGAGTTTG
*
4196753 AAATAACTCAAAATCA
1 AAATAATTCAAAATCA
* *
4196769 AAATTATTCAAATTCA
1 AAATAATTCAAAATCA
4196785 AAATAATTCAAAA
1 AAATAATTCAAAA
4196798 AATTTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAAATCA
Found at i:4200952 original size:20 final size:20
Alignment explanation
Indices: 4200924--4200961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4200914 TTTAATTAAT
*
4200924 TTAGCTTAATTAACTTAAAC
1 TTAGCTTAATTAAATTAAAC
*
4200944 TTAGTTTAATTAAATTAA
1 TTAGCTTAATTAAATTAA
4200962 GCTAATCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAGCTTAATTAAATTAAAC
Found at i:4206985 original size:14 final size:14
Alignment explanation
Indices: 4206966--4207004 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4206956 GAAAAGAAGC
* *
4206966 TATATATATATAGA
1 TATATATATACACA
4206980 TATATATATACACA
1 TATATATATACACA
*
4206994 CATATATATAC
1 TATATATATAC
4207005 TGTTGGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (14 bp):
TATATATATACACA
Found at i:4207736 original size:32 final size:32
Alignment explanation
Indices: 4207700--4207763 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4207690 TGCTTATATT
4207700 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
1 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
4207732 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
1 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
4207764 ATAGTGGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.03, T:0.31
Consensus pattern (32 bp):
CTAAAGCTCCAAACAATTCTTAAATTATTCCA
Found at i:4207931 original size:25 final size:25
Alignment explanation
Indices: 4207881--4207932 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
4207871 TTATGTAAAG
* * **
4207881 AAATATTTCATAAATAATGATGAAT
1 AAATAATTCATAAATAATAACAAAT
4207906 AAATAATTCATAAATAATAACAAAT
1 AAATAATTCATAAATAATAACAAAT
4207931 AA
1 AA
4207933 CTCGAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATAATTCATAAATAATAACAAAT
Found at i:4209180 original size:15 final size:15
Alignment explanation
Indices: 4209136--4209181 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4209126 TCATGTTACA
4209136 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
* *
4209151 TTTTA--AATGTTATG
1 TTTTAGTCA-CTTATG
4209165 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
4209180 TT
1 TT
4209182 ATTATTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTTAGTCACTTATG
Found at i:4220068 original size:15 final size:14
Alignment explanation
Indices: 4220042--4220087 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
4220032 GAAAATTAAT
4220042 ATAAAATCTAAAATA
1 ATAAAAT-TAAAATA
*
4220057 ATAATAATTAAAAAAA
1 ATAA-AATT-AAAATA
4220073 ATAAAATTAAAATA
1 ATAAAATTAAAATA
4220087 A
1 A
4220088 ACTTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
15 9 0.33
16 12 0.44
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAATTAAAATA
Found at i:4220086 original size:11 final size:11
Alignment explanation
Indices: 4220033--4220102 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
4220023 ATAGTTTAAG
*
4220033 AAAATTAATAT
1 AAAATTAAAAT
4220044 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
4220056 AATAA-T-AATT
1 AA-AATTAAAAT
4220066 AAAA--AAAAT
1 AAAATTAAAAT
4220075 AAAATTAAAAT
1 AAAATTAAAAT
*
4220086 AAACTTAAAAT
1 AAAATTAAAAT
*
4220097 AGAATT
1 AAAATT
4220103 TCTTATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 9 0.19
10 5 0.10
11 25 0.52
12 7 0.15
13 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:4223791 original size:23 final size:23
Alignment explanation
Indices: 4223709--4223795 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
4223699 CCTGATCAGT
*
4223709 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
4223731 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
4223751 ATACGACACACGATGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
4223774 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
4223796 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.61
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:4233639 original size:24 final size:23
Alignment explanation
Indices: 4233603--4233648 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
4233593 TATATTAGTG
*
4233603 AAAGATTTATTGATCAGAAGCAT
1 AAAGATTTATTGAGCAGAAGCAT
* *
4233626 AAAGAATTTCTTGAGCTGAAGCA
1 AAAG-ATTTATTGAGCAGAAGCA
4233649 AGGTAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (23 bp):
AAAGATTTATTGAGCAGAAGCAT
Found at i:4239080 original size:46 final size:46
Alignment explanation
Indices: 4239030--4239205 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
4239020 TGGTTGAGCA
4239030 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4239076 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
4239121 CATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4239169 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4239206 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 28 0.25
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4239186 original size:93 final size:93
Alignment explanation
Indices: 4239027--4239198 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
4239017 GGATGGTTGA
*
4239027 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
4239092 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
4239120 GCATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
4239185 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
4239199 CTTATGGGCG
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:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:4241036 original size:46 final size:44
Alignment explanation
Indices: 4240933--4241040 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 44
4240923 TGTCTTTGAC
** * *
4240933 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAATGCCATATATAAT
*
4240977 ATGGACTTACATGGCTCAATCCTGTCTCCAGA-GCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCA-ATGCCATA--TATAAT
4241023 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
4241041 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 32 0.57
45 1 0.02
46 23 0.41
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAATGCCATATATAAT
Found at i:4248360 original size:44 final size:45
Alignment explanation
Indices: 4248307--4248408 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
4248297 TGTCTTTGAC
* * *
4248307 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
4248351 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
4248397 ATGGA-TTACATG
1 ATGGACTTACATG
4248409 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 33 0.66
45 7 0.14
46 10 0.20
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:4254081 original size:17 final size:17
Alignment explanation
Indices: 4254059--4254092 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4254049 ATCCACTAAT
*
4254059 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4254076 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4254093 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4258720 original size:17 final size:17
Alignment explanation
Indices: 4258698--4258731 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4258688 ATCCACTAAT
*
4258698 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4258715 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4258732 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4259365 original size:48 final size:48
Alignment explanation
Indices: 4259294--4259391 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
4259284 TAATAAAACA
4259294 CTAATATTTAACTATCTAACTAAAATTAAAAATAAATTTAATTTGAAG
1 CTAATATTTAACTATCTAACTAAAATTAAAAATAAATTTAATTTGAAG
*
4259342 CTAATATTTAACTATCTAACTAAAATTAAAAATAGATTTAATTTGAAG
1 CTAATATTTAACTATCTAACTAAAATTAAAAATAAATTTAATTTGAAG
4259390 CT
1 CT
4259392 TTTTTCTGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (48 bp):
CTAATATTTAACTATCTAACTAAAATTAAAAATAAATTTAATTTGAAG
Found at i:4259751 original size:21 final size:21
Alignment explanation
Indices: 4259707--4259751 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4259697 ATATATATTC
* ** *
4259707 TAAATTTTTTTTTTCAGGATT
1 TAAATTTTTTTTTCCAAAAAT
4259728 TAAATTTTTTTTTCCAAAAAT
1 TAAATTTTTTTTTCCAAAAAT
4259749 TAA
1 TAA
4259752 TAAAATTATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (21 bp):
TAAATTTTTTTTTCCAAAAAT
Found at i:4270710 original size:82 final size:84
Alignment explanation
Indices: 4270604--4270829 Score: 227
Period size: 81 Copynumber: 2.7 Consensus size: 84
4270594 GGGCCTTGGT
* *
4270604 CCCTAAAAATAAAAA-A--TTCAATTTAATCCTCTTATAAATAGAAAATTTATAAA-TATATATA
1 CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATA-AAAAATTATAAATTA-ATATA
* *
4270665 TAGTGAAATTGCACTTTA-AC
64 TAGTAAAATTACACTTTAGAC
* * * *
4270685 CTCTTAAAAT-AAAAT-TTTTTAATTTAGTCTTCTTATAAATAAAAAATTATAAATTAATATATA
1 CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATAAAAAATTATAAATTAATATATA
*
4270748 GTAAAATTACACTTTAGCC
66 GTAAAATTACACTTTAGAC
** *
4270767 CCCTAAAAATAAAAATATTTTTTGTTTAATCCT-TTA-AAAAAATGATGAAATTATAAATTAATA
1 CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATAA--A--AAATTATAAATTAATA
4270830 CAAAATAATT
Statistics
Matches: 118, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
80 4 0.03
81 40 0.34
82 37 0.31
83 8 0.07
84 13 0.11
86 16 0.14
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.38
Consensus pattern (84 bp):
CCCTAAAAATAAAAATATTTTTAATTTAATCCTCTTATAAATAAAAAATTATAAATTAATATATA
GTAAAATTACACTTTAGAC
Found at i:4286309 original size:47 final size:46
Alignment explanation
Indices: 4286198--4286387 Score: 173
Period size: 47 Copynumber: 3.9 Consensus size: 46
4286188 TGCACATAGT
* * * ** * *
4286198 CACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTATACGGAT
1 CACATATCAC--ACTGATGCCATATCCCAGATATGGTCTTATACGAAG
* *
4286246 CACATATCACACTGATGTCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATAC-GAAG
*
4286293 CACATATCACACTGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATAC-GAAG
* * * *
4286340 CACAAATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACG
1 CACATATCACA---CT--GATGCCATATCCCAGATATGGTCTTATACG
4286388 GAAATCACAT
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
46 26 0.22
47 55 0.46
48 10 0.08
50 2 0.02
51 1 0.01
52 25 0.21
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (46 bp):
CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGAAG
Found at i:4291964 original size:13 final size:13
Alignment explanation
Indices: 4291946--4291972 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4291936 AAAATGAACT
4291946 ATTATCAATGGAC
1 ATTATCAATGGAC
4291959 ATTATCAATGGAC
1 ATTATCAATGGAC
4291972 A
1 A
4291973 GCCTTGTGTA
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTATCAATGGAC
Found at i:4301101 original size:44 final size:44
Alignment explanation
Indices: 4301053--4301136 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
4301043 GTAGTAATCA
4301053 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
1 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
4301097 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCT
1 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCT
4301137 GGTTTTGCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (44 bp):
TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
Found at i:4305377 original size:16 final size:17
Alignment explanation
Indices: 4305356--4305391 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
4305346 TTGAGATTAA
4305356 TTTAAAATTTTAAT-TT
1 TTTAAAATTTTAATATT
4305372 TTTAAAATTTTAATATT
1 TTTAAAATTTTAATATT
4305389 TTT
1 TTT
4305392 GCTTCAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAAATTTTAATATT
Found at i:4307019 original size:16 final size:16
Alignment explanation
Indices: 4306994--4307026 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4306984 CTCTTTCTGA
4306994 TTGTTTCTTTTT-TTT
1 TTGTTTCTTTTTATTT
4307009 TTGTATTCTTTTTATTT
1 TTGT-TTCTTTTTATTT
4307026 T
1 T
4307027 AATGGTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (16 bp):
TTGTTTCTTTTTATTT
Found at i:4314109 original size:30 final size:30
Alignment explanation
Indices: 4314074--4314134 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4314064 ACGCACCATC
4314074 TATCCAAACTCACCTAAGTAAACTTCAATA
1 TATCCAAACTCACCTAAGTAAACTTCAATA
4314104 TATCCAAACTCACCTAAGTAAACTTCAATA
1 TATCCAAACTCACCTAAGTAAACTTCAATA
4314134 T
1 T
4314135 TATTCAAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.28
Consensus pattern (30 bp):
TATCCAAACTCACCTAAGTAAACTTCAATA
Found at i:4319960 original size:18 final size:18
Alignment explanation
Indices: 4319937--4319977 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
4319927 AAATAATTTT
4319937 TAATTTTTTTAAAAAATA
1 TAATTTTTTTAAAAAATA
4319955 TAATTTTTTTAAAAAATA
1 TAATTTTTTTAAAAAATA
4319973 -AATTT
1 TAATTT
4319978 AAAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTTTTTTAAAAAATA
Found at i:4320127 original size:3 final size:3
Alignment explanation
Indices: 4320119--4320146 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4320109 GCTAAAATGT
4320119 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4320147 AACCGATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4325534 original size:13 final size:12
Alignment explanation
Indices: 4325508--4325540 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
4325498 GAGAACTTAA
4325508 GAAAA-TTTTAG
1 GAAAATTTTTAG
4325519 GAAAATTTTCTAG
1 GAAAATTTT-TAG
4325532 GAAAATTTT
1 GAAAATTTT
4325541 GTGCTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 3 0.15
13 12 0.60
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (12 bp):
GAAAATTTTTAG
Found at i:4329472 original size:46 final size:46
Alignment explanation
Indices: 4329408--4329557 Score: 158
Period size: 46 Copynumber: 3.1 Consensus size: 46
4329398 ACACACTGTA
*
4329408 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
* * * * *
4329454 GCCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTCTTACAC-GAATCACAT-ATCAC--A--T-TGAT
*
4329507 GCCATAGCCCAGCTACGGTCTTACAC-AGATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATCACATTGAT
4329553 GCCAT
1 GCCAT
4329558 GATCCAACCA
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
46 31 0.37
47 8 0.10
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.07
52 6 0.07
53 26 0.31
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (46 bp):
GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
Found at i:4330728 original size:23 final size:22
Alignment explanation
Indices: 4330640--4330746 Score: 114
Period size: 21 Copynumber: 5.0 Consensus size: 22
4330630 CCTGATCAGT
*
4330640 ATACGACACATAA-GTGCCTGA
1 ATACGACACACAAGGTGCCTGA
* *
4330661 A-ACGACACACGAGGTACCTGA
1 ATACGACACACAAGGTGCCTGA
* *
4330682 A-ACAACACACGAGGTGCCTG-
1 ATACGACACACAAGGTGCCTGA
4330702 ATACGACACACAAGGTGCCTGAA
1 ATACGACACACAAGGTGCCTG-A
* *
4330725 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAGGTGCCTGA
4330747 TCAGTATAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
20 10 0.14
21 43 0.59
22 1 0.01
23 19 0.26
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (22 bp):
ATACGACACACAAGGTGCCTGA
Found at i:4330983 original size:28 final size:29
Alignment explanation
Indices: 4330951--4331054 Score: 167
Period size: 29 Copynumber: 3.7 Consensus size: 29
4330941 AACACACCAG
* *
4330951 TATAATCC-TCCAAAACACACCAGTATCA
1 TATAATCCATCCAAAACACACCAGAATAA
*
4330979 TATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
4331007 TATAATCCATCCAAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
4331036 TATAATCCATCCAAAACAC
1 TATAATCCATCCAAAACAC
4331055 CAGGAATAGC
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
28 33 0.46
29 38 0.54
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:4331023 original size:57 final size:56
Alignment explanation
Indices: 4330951--4331062 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 56
4330941 AACACACCAG
* *
4330951 TATAATCCTCCAAAACACACCAGTATCATATAATCC-TCCCAAACACACCA-GAATAA
1 TATAATCCTCCAAAACACACCAGAATAATATAATCCAT-CCAAA-ACACCAGGAATAA
4331007 TATAATCCATCCAAAACACACCAGAATAATATAATCCATCCAAAACACCAGGAATA
1 TATAATCC-TCCAAAACACACCAGAATAATATAATCCATCCAAAACACCAGGAATA
4331063 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
56 14 0.27
57 36 0.71
58 1 0.02
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.19
Consensus pattern (56 bp):
TATAATCCTCCAAAACACACCAGAATAATATAATCCATCCAAAACACCAGGAATAA
Found at i:4336781 original size:46 final size:47
Alignment explanation
Indices: 4336716--4336863 Score: 203
Period size: 46 Copynumber: 3.2 Consensus size: 47
4336706 TTATCTTTGA
* * * * * *
4336716 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
4336762 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
4336808 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
4336854 CAGGTTGCCA
1 CATGTTGCCA
4336864 CATTTCATAT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.04
46 90 0.96
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.39
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
Found at i:4336867 original size:20 final size:20
Alignment explanation
Indices: 4336842--4336883 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4336832 CATGGTCTTA
4336842 CACATTTCATATCAGGTTGC
1 CACATTTCATATCAGGTTGC
4336862 CACATTTCATATCAGGTTGC
1 CACATTTCATATCAGGTTGC
4336882 CA
1 CA
4336884 TGGTGTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (20 bp):
CACATTTCATATCAGGTTGC
Found at i:4336871 original size:66 final size:66
Alignment explanation
Indices: 4336796--4336929 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
4336786 CATGGTCTTA
*
4336796 CACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTG
1 CACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTG
4336861 C
66 C
*
4336862 CACATTTCATATCAGGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGCTG
1 CACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTG
4336927 C
66 C
4336928 CA
1 CA
4336930 TGGTATCTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (66 bp):
CACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTG
C
Found at i:4336914 original size:46 final size:46
Alignment explanation
Indices: 4336862--4337009 Score: 278
Period size: 46 Copynumber: 3.2 Consensus size: 46
4336852 ATCAGGTTGC
* *
4336862 CACATTTCATATCAGGTTGCCATGGTGTCTTTCAACCATGGTCTTA
1 CACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTA
4336908 CACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTA
1 CACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTA
4336954 CACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTA
1 CACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTA
4337000 CACATTTCAT
1 CACATTTCAT
4337010 TTCAAAGAGC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 100 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (46 bp):
CACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTA
Found at i:4336942 original size:158 final size:158
Alignment explanation
Indices: 4336721--4337009 Score: 499
Period size: 158 Copynumber: 1.8 Consensus size: 158
4336711 TTTGACATGA
* * * * *
4336721 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTGTCTTTCAACCATGGTCTTACACATTTTCTATCAGGCTGCCATGGTATCTTTCAAC
*
4336786 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
4336851 TATCAGGTTGCCACATTTCATATCAGGT
131 TATCAGGTTGCCACATTTCATATCAGGT
*
4336879 TGCCATGGTGTCTTTCAACCATGGTCTTACACA-TTTCATATCAGGCTGCCATGGTATCTTTCAA
1 TGCCATAGTGTCTTTCAACCATGGTCTTACACATTTTC-TATCAGGCTGCCATGGTATCTTTCAA
4336943 CCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
65 CCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
4337008 AT
130 AT
4337010 TTCAAAGAGC
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
157 4 0.03
158 119 0.97
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (158 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTACACATTTTCTATCAGGCTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGGTTGCCACATTTCATATCAGGT
Found at i:4336949 original size:112 final size:112
Alignment explanation
Indices: 4336765--4336975 Score: 395
Period size: 112 Copynumber: 1.9 Consensus size: 112
4336755 TTTCTGTCAT
*
4336765 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCA
*
4336830 ACCATGGTCTTACACATTTCATATCAGGTTGCCACATTTCATATCAG
66 ACCATGGTCTTACACATTTCATATCAGGCTGCCACATTTCATATCAG
*
4336877 GTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCA
4336942 ACCATGGTCTTACACATTTCATATCAGGCTGCCA
66 ACCATGGTCTTACACATTTCATATCAGGCTGCCA
4336976 TGGTATCTTT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 96 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (112 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCA
ACCATGGTCTTACACATTTCATATCAGGCTGCCACATTTCATATCAG
Found at i:4339478 original size:30 final size:30
Alignment explanation
Indices: 4339411--4339478 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
4339401 CACCCTTAAA
* * *
4339411 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
4339441 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
4339470 AGTATTTAC
1 A-TATTTAC
4339479 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:4342234 original size:46 final size:46
Alignment explanation
Indices: 4342174--4342442 Score: 441
Period size: 46 Copynumber: 5.8 Consensus size: 46
4342164 TTTGACATGA
* * * * * *
4342174 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
4342220 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4342266 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
4342312 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
4342358 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4342404 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
4342443 TTCAAAGAGC
Statistics
Matches: 213, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 4 0.02
46 209 0.98
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:4344637 original size:38 final size:39
Alignment explanation
Indices: 4344546--4344680 Score: 109
Period size: 39 Copynumber: 3.4 Consensus size: 39
4344536 ACAAATATGG
*
4344546 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* *
4344585 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTT-A
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
4344622 GTACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 -CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
4344664 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
4344681 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
37 1 0.01
38 18 0.24
39 36 0.48
40 4 0.05
41 15 0.20
42 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:4346627 original size:44 final size:41
Alignment explanation
Indices: 4346551--4346631 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 41
4346541 ATCAATTAAG
4346551 TAATCATAATAATTTAATATAAAACTATAATAACAATCATTA
1 TAATCATAATAATTTAATATAAAACTATAATAA-AATCATTA
4346593 TAAT-ATATATAATTTAATATATAAAACCTA-AATAAAATC
1 TAATCATA-ATAATTT-A-ATATAAAA-CTATAATAAAATC
4346632 TTTGATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
41 3 0.09
42 11 0.31
43 5 0.14
44 13 0.37
45 3 0.09
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (41 bp):
TAATCATAATAATTTAATATAAAACTATAATAAAATCATTA
Done.