Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 51 of 97
Found at i:20558664 original size:2 final size:2
Alignment explanation
Indices: 20558659--20558684 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20558649 ACACACACAC
20558659 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
20558685 GTATGTATCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20563571 original size:42 final size:42
Alignment explanation
Indices: 20563524--20563613 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
20563514 TAGAAGTGTG
*
20563524 CATAAGTTGATGCTGACCCAGCTATGTGCGAGTGGGAGTGCC
1 CATAAGTTGATGCTGACCCAGCTATGTGCGAGTGGGAGTGCA
* *
20563566 CATAAGTTGATGCTGACTCGGCTATGTGCGAGTGGGAGTGCA
1 CATAAGTTGATGCTGACCCAGCTATGTGCGAGTGGGAGTGCA
20563608 CATAAG
1 CATAAG
20563614 CCGATGCGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
CATAAGTTGATGCTGACCCAGCTATGTGCGAGTGGGAGTGCA
Found at i:20563667 original size:2 final size:2
Alignment explanation
Indices: 20563660--20563753 Score: 127
Period size: 2 Copynumber: 46.0 Consensus size: 2
20563650 CATGATGATT
20563660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
**
20563702 GTA GTA GN TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20563746 TA CA TA TA
1 TA TA TA TA
20563754 CGGTGTATGG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
1 1 0.01
2 76 0.92
3 6 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:20576531 original size:68 final size:68
Alignment explanation
Indices: 20576405--20576531 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 68
20576395 ATCTCATAAG
* * *
20576405 GTATATGGAAAATACATCATATACATAATCTCATGGCATTCATCATGCTTTCTCAATCATCTCAT
1 GTATATGGAAAATACATCATATACATAATCTCATGGCATTCATCATACATACTCAATCATCTCAT
20576470 GTC
66 GTC
* * * * *
20576473 GTATATGGAATATACATCATGTACATTATCTCATGGCATTTATCATACATACTTAATCA
1 GTATATGGAAAATACATCATATACATAATCTCATGGCATTCATCATACATACTCAATCA
20576532 CCTTATATGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (68 bp):
GTATATGGAAAATACATCATATACATAATCTCATGGCATTCATCATACATACTCAATCATCTCAT
GTC
Found at i:20589392 original size:20 final size:20
Alignment explanation
Indices: 20589375--20589412 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20589365 CCTCAAATCT
20589375 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
*
20589395 TACTCTAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
20589413 GGGGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:20591232 original size:20 final size:20
Alignment explanation
Indices: 20591195--20591233 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20591185 TTAGTAAGTT
*
20591195 ATTTTAATTTTATGTTATTC
1 ATTTTAATTTTATATTATTC
20591215 ATTTT-ATTTTATTATTATT
1 ATTTTAATTTTA-TATTATT
20591234 TACTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTAATTTTATATTATTC
Found at i:20594735 original size:9 final size:9
Alignment explanation
Indices: 20594721--20594752 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20594711 ACACGATTAA
20594721 TAACACGTT
1 TAACACGTT
*
20594730 TAACACGAT
1 TAACACGTT
20594739 TAACACGTT
1 TAACACGTT
20594748 TAACA
1 TAACA
20594753 TGATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
TAACACGTT
Found at i:20594735 original size:21 final size:21
Alignment explanation
Indices: 20594711--20594759 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 21
20594701 ATACGACACG
20594711 ACACGATTAATAACACGTTTA
1 ACACGATTAATAACACGTTTA
20594732 ACACGA-T--TAACACGTTTA
1 ACACGATTAATAACACGTTTA
*
20594750 ACATGATTAA
1 ACACGATTAA
20594760 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 16 0.67
19 1 0.04
20 1 0.04
21 6 0.25
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (21 bp):
ACACGATTAATAACACGTTTA
Found at i:20594744 original size:18 final size:18
Alignment explanation
Indices: 20594721--20594759 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20594711 ACACGATTAA
20594721 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
*
20594739 TAACACGTTTAACATGAT
1 TAACACGTTTAACACGAT
20594757 TAA
1 TAA
20594760 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:20594759 original size:9 final size:9
Alignment explanation
Indices: 20594721--20594759 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
20594711 ACACGATTAA
*
20594721 TAACACGTT
1 TAACACGAT
20594730 TAACACGAT
1 TAACACGAT
*
20594739 TAACACGTT
1 TAACACGAT
*
20594748 TAACATGAT
1 TAACACGAT
20594757 TAA
1 TAA
20594760 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:20595045 original size:18 final size:18
Alignment explanation
Indices: 20595018--20595063 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
20595008 TGGCACGTAT
*
20595018 ACACGTTTAAACACGATA
1 ACACGATTAAACACGATA
* *
20595036 ACATGATTAAACATGATA
1 ACACGATTAAACACGATA
20595054 ACACGATTAA
1 ACACGATTAA
20595064 GTAAATGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:20597060 original size:61 final size:61
Alignment explanation
Indices: 20596965--20597187 Score: 320
Period size: 61 Copynumber: 3.7 Consensus size: 61
20596955 AGCTCATGTA
* * * *
20596965 CATCATCACCGGCATGTGCACTGCCTACTCCGCACATGCACTGTTGTAATTTTCATGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACTGTTGTAATTATCACGACAG
* *
20597026 CATCATTACCGGCATGTGCACTGCCTACTCCGCACATGCACTGTTGTAATTATCACGACAT
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACTGTTGTAATTATCACGACAG
** * ** *
20597087 CATCATTGTCGACATGTGCACTGCCCACTCCGCACATGCACAATTGTAACTATCACGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACTGTTGTAATTATCACGACAG
* *
20597148 CATCATTACTGGCATGTGCACTGCCCACTTCGCACATGCA
1 CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCA
20597188 TGGTTGCATT
Statistics
Matches: 145, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 145 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (61 bp):
CATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACTGTTGTAATTATCACGACAG
Found at i:20599224 original size:37 final size:37
Alignment explanation
Indices: 20599157--20599227 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
20599147 GGGTATTATA
*
20599157 GTGCACTCCCTACTCGCACACTCTATCATCATCATGT
1 GTGCACTCCCTACTCGCACACTCTAACATCATCATGT
*
20599194 GTGCACTCCCTACTTGCACACT-TCAACATCATCA
1 GTGCACTCCCTACTCGCACACTCT-AACATCATCA
20599228 CACAACATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.24, C:0.38, G:0.10, T:0.28
Consensus pattern (37 bp):
GTGCACTCCCTACTCGCACACTCTAACATCATCATGT
Found at i:20604318 original size:74 final size:74
Alignment explanation
Indices: 20604204--20604352 Score: 262
Period size: 74 Copynumber: 2.0 Consensus size: 74
20604194 ATGAAGTTGA
* * *
20604204 AAACAGTGGGTATAAACTCAGTTAGTGAACAAAGGAAGGGAACAAGCAAACGATAAGAAAAGTTT
1 AAACAGTGAGTATAAACCCAGTGAGTGAACAAAGGAAGGGAACAAGCAAACGATAAGAAAAGTTT
*
20604269 AATGAAATC
66 AAAGAAATC
20604278 AAACAGTGAGTATAAACCCAGTGAGTGAACAAAGGAAGGGAACAAGCAAACGATAAGAAAAGTTT
1 AAACAGTGAGTATAAACCCAGTGAGTGAACAAAGGAAGGGAACAAGCAAACGATAAGAAAAGTTT
20604343 AAAGAAATC
66 AAAGAAATC
20604352 A
1 A
20604353 TGATGCACTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.15
Consensus pattern (74 bp):
AAACAGTGAGTATAAACCCAGTGAGTGAACAAAGGAAGGGAACAAGCAAACGATAAGAAAAGTTT
AAAGAAATC
Found at i:20620125 original size:63 final size:63
Alignment explanation
Indices: 20620023--20620204 Score: 276
Period size: 63 Copynumber: 2.9 Consensus size: 63
20620013 GAAATTGATG
*
20620023 CAACCGTGCATGTGCGAAGTGGGAAGTGCAATGCTAGTTGAATGACAAAGGATGTGATAATTA
1 CAACCGTGCATGTGCGAAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
* * *
20620086 CGACCGTGCATGT-CTGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAAGATGTGATAATTA
1 CAACCGTGCATGTGC-GAAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
* * * *
20620149 CAACCGTGCATGTGCGAAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGTTGTG
1 CAACCGTGCATGTGCGAAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTG
20620205 GGGACGGCAA
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
62 1 0.01
63 104 0.98
64 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (63 bp):
CAACCGTGCATGTGCGAAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
Found at i:20626866 original size:22 final size:23
Alignment explanation
Indices: 20626823--20626869 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
20626813 ATATAGAGTT
20626823 ATTTAGGCTTAATTTTGATAGTA
1 ATTTAGGCTTAATTTTGATAGTA
*
20626846 ATTTA-GCTTAGTTCTTG-TAGTA
1 ATTTAGGCTTAATT-TTGATAGTA
20626868 AT
1 AT
20626870 GCATAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (23 bp):
ATTTAGGCTTAATTTTGATAGTA
Found at i:20642673 original size:21 final size:21
Alignment explanation
Indices: 20642634--20642673 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20642624 ATAAAATATT
*
20642634 AAAAGACTAAATTGGAAAAGA
1 AAAAGACTAAATTCGAAAAGA
* *
20642655 AAAAGACTGAATTCTAAAA
1 AAAAGACTAAATTCGAAAA
20642674 TAAAGAAAAT
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:0.60, C:0.07, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAAGACTAAATTCGAAAAGA
Found at i:20643435 original size:2 final size:2
Alignment explanation
Indices: 20643428--20643466 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
20643418 TAAATATAAG
*
20643428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20643467 TTCAAACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20643671 original size:35 final size:35
Alignment explanation
Indices: 20643620--20643797 Score: 149
Period size: 36 Copynumber: 4.9 Consensus size: 35
20643610 TGGCATACAT
* *
20643620 CATCATCATCGTGTGCACTCTCATACCACACACCA
1 CATCATCATCATGTGCACTCTCACACCACACACCA
* * * *
20643655 CATCCTCATCATGTGCACTCCCACACCGCACATGGCAA
1 CATCATCATCATGTGCACTCTCACACCACACA---CCA
* *
20643693 TATCATCATCATGTGCACTCTCACACTACACACCA
1 CATCATCATCATGTGCACTCTCACACCACACACCA
* * * **
20643728 CCCTCACCGTCATGTGCACTCTCACACTGCACACCA
1 -CATCATCATCATGTGCACTCTCACACCACACACCA
* * * * *
20643764 CCCTCACCGTCATGTGCACTCCCACACCGCACAC
1 -CATCATCATCATGTGCACTCTCACACCACACAC
20643798 GCACGATTAT
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
35 29 0.24
36 62 0.52
38 29 0.24
ACGTcount: A:0.26, C:0.44, G:0.10, T:0.20
Consensus pattern (35 bp):
CATCATCATCATGTGCACTCTCACACCACACACCA
Found at i:20643673 original size:77 final size:71
Alignment explanation
Indices: 20643584--20643760 Score: 219
Period size: 73 Copynumber: 2.4 Consensus size: 71
20643574 TAACTAATAC
* * *
20643584 CATCATGTGCACTCCCACACCGTACATGGCATACATCATCATCATCGTGTGCACTCTCATACCAC
1 CATCATGTGCACTCCCACACCGCACATGGC--A-AT-ATCATCATCATGTGCACTCTCACACCAC
20643649 ACACCACATCCT
62 ACACCAC--CCT
*
20643661 CATCATGTGCACTCCCACACCGCACATGGCAATATCATCATCATGTGCACTCTCACACTACACAC
1 CATCATGTGCACTCCCACACCGCACATGGCAATATCATCATCATGTGCACTCTCACACCACACAC
20643726 CACCCT
66 CACCCT
* *
20643732 CACCGTCATGTGCACTCTCACACTGCACA
1 CA---TCATGTGCACTCCCACACCGCACA
20643761 CCACCCTCAC
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
71 5 0.05
73 32 0.35
74 24 0.26
75 1 0.01
77 29 0.32
ACGTcount: A:0.27, C:0.40, G:0.11, T:0.22
Consensus pattern (71 bp):
CATCATGTGCACTCCCACACCGCACATGGCAATATCATCATCATGTGCACTCTCACACCACACAC
CACCCT
Found at i:20643748 original size:36 final size:36
Alignment explanation
Indices: 20643701--20643790 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
20643691 AATATCATCA
20643701 TCATGTGCACTCTCACACTACACACCACCCTCACCG
1 TCATGTGCACTCTCACACTACACACCACCCTCACCG
*
20643737 TCATGTGCACTCTCACACTGCACACCACCCTCACCG
1 TCATGTGCACTCTCACACTACACACCACCCTCACCG
*
20643773 TCATGTGCACTCCCACAC
1 TCATGTGCACTCTCACAC
20643791 CGCACACGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.47, G:0.10, T:0.20
Consensus pattern (36 bp):
TCATGTGCACTCTCACACTACACACCACCCTCACCG
Found at i:20643796 original size:36 final size:36
Alignment explanation
Indices: 20643663--20643797 Score: 153
Period size: 36 Copynumber: 3.7 Consensus size: 36
20643653 CACATCCTCA
* *** * *
20643663 TCATGTGCACTCCCACACCGCACATGGCAATATCATCA
1 TCATGTGCACTCCCACACCGCACA--CCACCCTCACCG
* **
20643701 TCATGTGCACTCTCACACTACACACCACCCTCACCG
1 TCATGTGCACTCCCACACCGCACACCACCCTCACCG
* *
20643737 TCATGTGCACTCTCACACTGCACACCACCCTCACCG
1 TCATGTGCACTCCCACACCGCACACCACCCTCACCG
20643773 TCATGTGCACTCCCACACCGCACAC
1 TCATGTGCACTCCCACACCGCACAC
20643798 GCACGATTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 64 0.75
38 21 0.25
ACGTcount: A:0.25, C:0.44, G:0.11, T:0.19
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACACCACCCTCACCG
Found at i:20645761 original size:14 final size:14
Alignment explanation
Indices: 20645742--20645781 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
20645732 TGTTTTTCAT
20645742 TTTCTTTTTCTTCC
1 TTTCTTTTTCTTCC
*
20645756 TTTCTTTTCCTTTCC
1 TTTCTTTTTC-TTCC
20645771 TTT-TTTTTCTT
1 TTTCTTTTTCTT
20645782 ACTTCTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 7 0.30
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTCTTTTTCTTCC
Found at i:20645790 original size:25 final size:25
Alignment explanation
Indices: 20645735--20645792 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20645725 ATCAATTTGT
* * *
20645735 TTTTCATTTTCTTTTTCTTCCTTTC
1 TTTTCCTTTCCTTTTTCTTCCTTAC
*
20645760 TTTTCCTTTCCTTTTT-TTTCTTAC
1 TTTTCCTTTCCTTTTTCTTCCTTAC
20645784 TTCTTCCTT
1 TT-TTCCTT
20645793 CTCTTATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTCCTTTCCTTTTTCTTCCTTAC
Found at i:20652405 original size:17 final size:17
Alignment explanation
Indices: 20652369--20652424 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
20652359 CTAAAAAAAA
* * *
20652369 TAAAGAAAATAACATCC
1 TAAATAAAATAAAATAC
*
20652386 TAAATAAACTAAAATAC
1 TAAATAAAATAAAATAC
* *
20652403 TAAATAAAATAGAATTC
1 TAAATAAAATAAAATAC
20652420 TAAAT
1 TAAAT
20652425 GCACTTGCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.25
Consensus pattern (17 bp):
TAAATAAAATAAAATAC
Found at i:20655355 original size:19 final size:19
Alignment explanation
Indices: 20655331--20655368 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20655321 CTGCCAAACT
*
20655331 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
*
20655350 CTCAAATCATACTTCAATA
1 CTCAAATCATACTCCAATA
20655369 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:20656735 original size:26 final size:27
Alignment explanation
Indices: 20656673--20656736 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
20656663 CTTAAAGTAC
*
20656673 TAAAATCCT-AATAAAAATAAAAAAAA
1 TAAAATCTTAAATAAAAATAAAAAAAA
*
20656699 TCACAAA--TTAAAT-AAAATAAAATAAA
1 T-A-AAATCTTAAATAAAAATAAAAAAAA
20656725 TAAAATCTTAAA
1 TAAAATCTTAAA
20656737 CCAACTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 20 0.65
27 4 0.13
28 3 0.10
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (27 bp):
TAAAATCTTAAATAAAAATAAAAAAAA
Found at i:20663437 original size:125 final size:127
Alignment explanation
Indices: 20663206--20663452 Score: 453
Period size: 125 Copynumber: 2.0 Consensus size: 127
20663196 GCACTGATCG
*
20663206 GTGCTCCCCTCTCTTGGGGAGCACTAGATCTGGTGCCCACTTGTTTTTTTTTTTTGTGGAAAAAA
1 GTGCTCCCCTCCCTTGGGGAGCACTAGATCTGGTGCCCACTTGTTTTTTTTTTTTGTGGAAAAAA
*
20663271 AACTATATAATAATAATTTTTATAATTAATAAAGAATAAAATTATCCTTTTGATATTGCCAT
66 AACTATATAATAATAATTTTTACAATTAATAAAGAATAAAATTATCCTTTTGATATTGCCAT
*
20663333 GTGCTCCCCTCCCTTGGGGAGCACTAGATCTGGTGCTCACTTG-TTTTTTTTTTT-TGGAAAAAA
1 GTGCTCCCCTCCCTTGGGGAGCACTAGATCTGGTGCCCACTTGTTTTTTTTTTTTGTGGAAAAAA
20663396 AACTATATAATAATAATTTTTACAATTAATAAAGAATAAAATTATCCTTTTGATATT
66 AACTATATAATAATAATTTTTACAATTAATAAAGAATAAAATTATCCTTTTGATATT
20663453 ATCATGTCAT
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
125 65 0.56
126 11 0.09
127 41 0.35
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (127 bp):
GTGCTCCCCTCCCTTGGGGAGCACTAGATCTGGTGCCCACTTGTTTTTTTTTTTTGTGGAAAAAA
AACTATATAATAATAATTTTTACAATTAATAAAGAATAAAATTATCCTTTTGATATTGCCAT
Found at i:20676837 original size:91 final size:93
Alignment explanation
Indices: 20676736--20676924 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 93
20676726 GAAAACTGCC
* *
20676736 GCATATCTGACTGTAAGAAAATAGGTTAGATAAAATAAATG-TCCATAATTTAGCCATGAA-TTT
1 GCATATCTGACTGTAAGAAAACAGGTTAGATAAAATAAATGCTCCATAATTTAGCCATGAACTTG
20676799 TAATTACTTCCCAAGATAAATAAAGGCT
66 TAATTACTTCCCAAGATAAATAAAGGCT
* *
20676827 GCATATCTGACTGTAAGATAACAGGTTAGATAGAATAAATGTCCTCCATAATTTAGCCATGAACT
1 GCATATCTGACTGTAAGAAAACAGGTTAGATAAAATAAATG--CTCCATAATTTAGCCATGAACT
* * *
20676892 TGTAATTACTTCCCAGGATAAATGATGGCT
64 TGTAATTACTTCCCAAGATAAATAAAGGCT
20676922 GCA
1 GCA
20676925 ACCTATGGGT
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
91 38 0.44
94 19 0.22
95 30 0.34
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (93 bp):
GCATATCTGACTGTAAGAAAACAGGTTAGATAAAATAAATGCTCCATAATTTAGCCATGAACTTG
TAATTACTTCCCAAGATAAATAAAGGCT
Found at i:20681500 original size:18 final size:18
Alignment explanation
Indices: 20681477--20681514 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
20681467 CCAAGATTGA
20681477 CATCATGGCCACCCAATG
1 CATCATGGCCACCCAATG
20681495 CATCATGGCCACCCAATG
1 CATCATGGCCACCCAATG
20681513 CA
1 CA
20681515 CAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.39, G:0.16, T:0.16
Consensus pattern (18 bp):
CATCATGGCCACCCAATG
Found at i:20683070 original size:21 final size:21
Alignment explanation
Indices: 20683026--20683069 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20683016 ACCAACTCTC
*
20683026 TTTCTCTTCTTCCTTTTCCTT
1 TTTCTCTTCTTCCTATTCCTT
*
20683047 TTTCTCTTCTTTC-ATTCCTT
1 TTTCTCTTCTTCCTATTCCTT
20683067 TTT
1 TTT
20683070 TGGCCAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCTCTTCTTCCTATTCCTT
Found at i:20685723 original size:13 final size:13
Alignment explanation
Indices: 20685707--20685781 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
20685697 GTTGGAGATG
20685707 TTTGTTAGAATAC
1 TTTGTTAGAATAC
*
20685720 TTTGTT-GCATTATC
1 TTTGTTAG-AATA-C
*
20685734 ATTTATTAGAATAC
1 -TTTGTTAGAATAC
*
20685748 TTTGTT-GCATTATC
1 TTTGTTAG-AATA-C
20685762 ATTTGTTAGAATAC
1 -TTTGTTAGAATAC
20685776 TTTGTT
1 TTTGTT
20685782 GCATTGATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
12 2 0.04
13 23 0.48
14 4 0.08
15 17 0.35
16 2 0.04
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.52
Consensus pattern (13 bp):
TTTGTTAGAATAC
Found at i:20685743 original size:28 final size:28
Alignment explanation
Indices: 20685711--20685786 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
20685701 GAGATGTTTG
20685711 TTAGAATACTTTGTTGCATTATCATTTA
1 TTAGAATACTTTGTTGCATTATCATTTA
*
20685739 TTAGAATACTTTGTTGCATTATCATTTG
1 TTAGAATACTTTGTTGCATTATCATTTA
20685767 TTAGAATACTTTGTTGCATT
1 TTAGAATACTTTGTTGCATT
20685787 GATAATGCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (28 bp):
TTAGAATACTTTGTTGCATTATCATTTA
Found at i:20685768 original size:15 final size:15
Alignment explanation
Indices: 20685720--20685768 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
20685710 GTTAGAATAC
20685720 TTTGTTGCATTATCA
1 TTTGTTGCATTATCA
* *
20685735 TTTATTAG-AATA-C-
1 TTTGTT-GCATTATCA
20685748 TTTGTTGCATTATCA
1 TTTGTTGCATTATCA
20685763 TTTGTT
1 TTTGTT
20685769 AGAATACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 1 0.04
13 8 0.31
14 2 0.08
15 14 0.54
16 1 0.04
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.55
Consensus pattern (15 bp):
TTTGTTGCATTATCA
Found at i:20685803 original size:2 final size:2
Alignment explanation
Indices: 20685796--20685841 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
20685786 TGATAATGCA
20685796 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
20685838 AT AT
1 AT AT
20685842 GACTATGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20698692 original size:15 final size:14
Alignment explanation
Indices: 20698673--20698700 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20698663 GTGTCAAATA
20698673 AAAAAAAAATTTTG
1 AAAAAAAAATTTTG
20698687 AAAAAAAAATTTTG
1 AAAAAAAAATTTTG
20698701 CCACATCAAT
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:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAAAAAAATTTTG
Found at i:20698764 original size:31 final size:31
Alignment explanation
Indices: 20698729--20698789 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
20698719 GTCATGTCAT
*
20698729 AATGACCAAATTACACAAAATACTAGAATAC
1 AATGACCAAATTAAACAAAATACTAGAATAC
* * * *
20698760 AATGACTAGATTAAACAAAATTCTATAATA
1 AATGACCAAATTAAACAAAATACTAGAATA
20698790 AAAAGATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.25
Consensus pattern (31 bp):
AATGACCAAATTAAACAAAATACTAGAATAC
Found at i:20709138 original size:28 final size:28
Alignment explanation
Indices: 20709096--20709151 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
20709086 GAAAAAATAT
20709096 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGCC
*
20709124 CCTGG-GGTGGCAAAATTACCATTTTGCC
1 CCTGGTGGTGG-AAAATTACAATTTTGCC
20709152 TCTATACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGCC
Found at i:20709224 original size:20 final size:20
Alignment explanation
Indices: 20709199--20709244 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
20709189 CTTCTAAACC
20709199 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
20709219 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
20709239 TCAAAT
1 TCAAAT
20709245 GGAGCCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:20717330 original size:17 final size:16
Alignment explanation
Indices: 20717303--20717338 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
20717293 ATAATAATAA
*
20717303 TAATAATAATATTTTG
1 TAATAATAATATTATG
20717319 TAATAGATAATATTATG
1 TAATA-ATAATATTATG
20717336 TAA
1 TAA
20717339 ATATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
TAATAATAATATTATG
Found at i:20722217 original size:109 final size:110
Alignment explanation
Indices: 20722025--20722236 Score: 345
Period size: 109 Copynumber: 1.9 Consensus size: 110
20722015 GTTAGAATGG
* * * * * *
20722025 CATGTTTTTTTTAACATTTTTTATTATAAATATGTATGGGAATTAGTCTTGATTCTTACATTTTG
1 CATGTTTTTGTTAACATTTTTTATTAGAAACATGAATAGGAATTAGTCTTAATTCTTACATTTTG
20722090 ATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCACGGCTTC
66 ATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCACGGCTTC
* *
20722135 CATGTTTTTGTTAACATTTTTTATT-GAAACATGAATAGGAATTAGTCTTAATTTTTATATTTTG
1 CATGTTTTTGTTAACATTTTTTATTAGAAACATGAATAGGAATTAGTCTTAATTCTTACATTTTG
20722199 ATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCA
66 ATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCA
20722237 TATGTATGAA
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 70 0.74
110 24 0.26
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.52
Consensus pattern (110 bp):
CATGTTTTTGTTAACATTTTTTATTAGAAACATGAATAGGAATTAGTCTTAATTCTTACATTTTG
ATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCACGGCTTC
Found at i:20729276 original size:2 final size:2
Alignment explanation
Indices: 20729269--20729313 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
20729259 NNNNNNNNNN
*
20729269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20729311 AT A
1 AT A
20729314 AATTATAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20731734 original size:19 final size:19
Alignment explanation
Indices: 20731710--20731747 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20731700 CCATTTAACT
*
20731710 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
20731729 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
20731748 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:20738314 original size:15 final size:14
Alignment explanation
Indices: 20738290--20738335 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
20738280 AGATCAGAGA
20738290 TTTTGATTTTAAAG
1 TTTTGATTTTAAAG
20738304 TTTTGGATTTTAAAG
1 TTTT-GATTTTAAAG
20738319 TTTT-ATGTTTTAAAG
1 TTTTGA--TTTTAAAG
20738334 TT
1 TT
20738336 GTTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.03
14 4 0.14
15 24 0.83
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
TTTTGATTTTAAAG
Found at i:20738395 original size:14 final size:15
Alignment explanation
Indices: 20738370--20738402 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20738360 TGCGTGACCC
20738370 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
20738385 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
20738399 AAGT
1 AAGT
20738403 CAGGTTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Found at i:20738409 original size:19 final size:19
Alignment explanation
Indices: 20738371--20738410 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20738361 GCGTGACCCA
*
20738371 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
*
20738390 AGTTAAGTTAAGTCAGGTT
1 AGTTAAGTTAAGTCAAGTT
20738409 AG
1 AG
20738411 GTAGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:20738412 original size:5 final size:5
Alignment explanation
Indices: 20738370--20738402 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
20738360 TGCGTGACCC
20738370 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGT
20738403 CAGGTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:20757988 original size:20 final size:20
Alignment explanation
Indices: 20757963--20758008 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
20757953 TTTTGACCCC
20757963 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
20757983 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
20758003 ATTTGA
1 ATTTGA
20758009 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:20758084 original size:28 final size:27
Alignment explanation
Indices: 20758053--20758105 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
20758043 TTTGGAGTAT
*
20758053 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
20758081 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
20758106 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:20758111 original size:28 final size:28
Alignment explanation
Indices: 20758053--20758111 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
20758043 TTTGGAGTAT
* *
20758053 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
20758081 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
20758109 AGG
1 AGG
20758112 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:20769968 original size:9 final size:9
Alignment explanation
Indices: 20769954--20769994 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
20769944 TTATTGGTCC
20769954 ATTTTAAAA
1 ATTTTAAAA
20769963 ATTTTAAAA
1 ATTTTAAAA
20769972 ATTTTAAAA
1 ATTTTAAAA
*
20769981 A-TTTAAAC
1 ATTTTAAAA
20769989 ATTTTA
1 ATTTTA
20769995 TCTCCACCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:20769977 original size:18 final size:17
Alignment explanation
Indices: 20769954--20769994 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
20769944 TTATTGGTCC
20769954 ATTTTAAAAATTTTAAAA
1 ATTTTAAAAA-TTTAAAA
*
20769972 ATTTTAAAAATTTAAAC
1 ATTTTAAAAATTTAAAA
20769989 ATTTTA
1 ATTTTA
20769995 TCTCCACCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTAAAAATTTAAAA
Found at i:20770192 original size:20 final size:20
Alignment explanation
Indices: 20770167--20770208 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
20770157 CTTCTAAATC
20770167 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
20770187 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
20770207 TC
1 TC
20770209 GAATGGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:20770845 original size:5 final size:5
Alignment explanation
Indices: 20770835--20770863 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
20770825 GGAGGAATGC
20770835 AGGAG AGGAG AGGAG AGGAG AGGAG AGGA
1 AGGAG AGGAG AGGAG AGGAG AGGAG AGGA
20770864 TAGGGACGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
AGGAG
Found at i:20779021 original size:23 final size:24
Alignment explanation
Indices: 20778995--20779040 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
20778985 TCACTCAACC
20778995 TTTGAAGATCTTAA-TCCA-AATAA
1 TTTGAAG-TCTTAATTCCATAATAA
*
20779018 TTTGATGTCTTAATTCCATAATA
1 TTTGAAGTCTTAATTCCATAATA
20779041 TGTCTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 10 0.50
24 4 0.20
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTGAAGTCTTAATTCCATAATAA
Found at i:20780784 original size:6 final size:6
Alignment explanation
Indices: 20780767--20780797 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20780757 TAAACTAAGA
*
20780767 ATTTAT AGTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT A
20780798 GATCATGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (6 bp):
ATTTAT
Found at i:20784216 original size:9 final size:9
Alignment explanation
Indices: 20784202--20784241 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
20784192 AATAATACGT
20784202 TTAACACGA
1 TTAACACGA
* *
20784211 TTAACATGT
1 TTAACACGA
*
20784220 TTAACACGT
1 TTAACACGA
20784229 TTAACACGA
1 TTAACACGA
20784238 TTAA
1 TTAA
20784242 ATAATAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (9 bp):
TTAACACGA
Found at i:20784241 original size:18 final size:18
Alignment explanation
Indices: 20784198--20784241 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20784188 GATTAATAAT
20784198 ACGTTTAACACGATTAAC
1 ACGTTTAACACGATTAAC
* *
20784216 ATGTTTAACACGTTTAAC
1 ACGTTTAACACGATTAAC
*
20784234 ACGATTAA
1 ACGTTTAA
20784242 ATAATAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (18 bp):
ACGTTTAACACGATTAAC
Found at i:20784282 original size:19 final size:20
Alignment explanation
Indices: 20784237--20784273 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20784227 GTTTAACACG
20784237 ATTAAATAATAATATTTATA
1 ATTAAATAATAATATTTATA
20784257 ATTAAAT-ATAAT-TTTAT
1 ATTAAATAATAATATTTAT
20784274 TATTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAATAATAATATTTATA
Found at i:20788939 original size:107 final size:106
Alignment explanation
Indices: 20788757--20788974 Score: 285
Period size: 107 Copynumber: 2.1 Consensus size: 106
20788747 CTTAATTAAC
*
20788757 TAAA-TTGTTTAATTAAATCATTGAGCCTAATTAATTAAATTGTTTAATTAAGTCATTAGGCCTA
1 TAAATTTGTTTAATTAAATCATTGAGCCTAATTAATTAAATTGTTTAATTAAATCATTAGGCCTA
*
20788821 ATTAATTAAATTAAACAATTAAGTTATTGGGCCTAATTGAT
66 ATTAATTAAATTAAACAATTAAGTTATTGAGCCTAATTGAT
* * * * ** * *
20788862 TAAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAATTGTTGGGCTT
1 TAAATTTGTTTAATTAAATCATTGAGCCTAATTAATT-AAATTGTTTAATTAAATCATTAGGCCT
**** *
20788927 AATTAATTAAATTGTTTAATTAAGTTATTGAGCCTGATTGAT
65 AATTAATTAAATTAAACAATTAAGTTATTGAGCCTAATTGAT
20788969 TAAATT
1 TAAATT
20788975 AAATAATTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 4 0.04
106 28 0.29
107 64 0.67
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (106 bp):
TAAATTTGTTTAATTAAATCATTGAGCCTAATTAATTAAATTGTTTAATTAAATCATTAGGCCTA
ATTAATTAAATTAAACAATTAAGTTATTGAGCCTAATTGAT
Found at i:20788982 original size:35 final size:35
Alignment explanation
Indices: 20788726--20788988 Score: 246
Period size: 35 Copynumber: 7.5 Consensus size: 35
20788716 CACTTGATTA
* * *
20788726 AAATTGTTTAATTAAG---TTGTGCTTAATTAACT
1 AAATTGTTTAATTAAGTTATTGAGCCTAATTAATT
* *
20788758 AAATTGTTTAATTAAATCATTGAGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGAGCCTAATTAATT
*
20788793 AAATTGTTTAATTAAGTCATT-AGGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGA-GCCTAATTAATT
**** * *
20788828 AAATTAAACAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGAGCCTAATTAATT
* * * *
20788863 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTTATTGAGCCTAATTAATT
* * * *
20788899 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGAGCCTAATTAATT
* *
20788935 AAATTGTTTAATTAAGTTATTGAGCCTGATTGATT
1 AAATTGTTTAATTAAGTTATTGAGCCTAATTAATT
***
20788970 AAATTAAATAATTAAGTTA
1 AAATTGTTTAATTAAGTTA
20788989 ATTGGGCTTC
Statistics
Matches: 191, Mismatches: 33, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
32 15 0.08
34 1 0.01
35 120 0.63
36 52 0.27
37 3 0.02
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGAGCCTAATTAATT
Found at i:20788996 original size:71 final size:69
Alignment explanation
Indices: 20788766--20788997 Score: 259
Period size: 71 Copynumber: 3.3 Consensus size: 69
20788756 CTAAATTGTT
* * * * *
20788766 TAATTAAATCATTGAGCCTAATTAATTAAATTGTTTAATTAAGTCATT-AGGCCTAATTAATTAA
1 TAATTAAGTTATTGGGCTTAATTAATTAAATTGTTTAATTAAGTCATTGA-GCCT-ATTGATTAA
20788830 ATTAAA
64 ATTAAA
* * * *
20788836 CAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATTAA
1 TAATTAAGTTATTGGGCTTAATTAATTAAA-TTGTTTAATTAAGTCATTGAGCCTA-TTGATT-A
***
20788901 AATTGTT
63 AATTAAA
* * *
20788908 TAATTAAATTGTTGGGCTTAATTAATTAAATTGTTTAATTAAGTTATTGAGCCTGATTGATTAAA
1 TAATTAAGTTATTGGGCTTAATTAATTAAATTGTTTAATTAAGTCATTGAGCCT-ATTGATTAAA
20788973 TTAAA
65 TTAAA
20788978 TAATTAAGTTAATTGGGCTT
1 TAATTAAGTT-ATTGGGCTT
20788998 CTAAAGGACT
Statistics
Matches: 134, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
70 40 0.30
71 63 0.47
72 31 0.23
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (69 bp):
TAATTAAGTTATTGGGCTTAATTAATTAAATTGTTTAATTAAGTCATTGAGCCTATTGATTAAAT
TAAA
Found at i:20791327 original size:51 final size:53
Alignment explanation
Indices: 20791251--20791360 Score: 188
Period size: 51 Copynumber: 2.1 Consensus size: 53
20791241 CATTATTGGT
*
20791251 AGGTTATTGCTTAATCTCATTAAAAAGCAAGAATCCCTTTGTGGA-T-TGTAA
1 AGGTTACTGCTTAATCTCATTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAA
*
20791302 AGGTTACTGCTTGATCTCATTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAA
1 AGGTTACTGCTTAATCTCATTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAA
20791355 AGGTTA
1 AGGTTA
20791361 TCACTTTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
51 43 0.78
52 1 0.02
53 11 0.20
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (53 bp):
AGGTTACTGCTTAATCTCATTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAA
Found at i:20792871 original size:32 final size:32
Alignment explanation
Indices: 20792834--20792916 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
20792824 TTACCCATTG
* *
20792834 GTTTATTGAGCTTGGTTTATTTGAGAAGCATC
1 GTTTATTAAGCTTGGTTTATTTGAGAAACATC
* * *
20792866 GTTTATTAAACTTAGTTTATTTGAGAAACATG
1 GTTTATTAAGCTTGGTTTATTTGAGAAACATC
20792898 GTTTATTAAGCTTGGTTTA
1 GTTTATTAAGCTTGGTTTA
20792917 GTTGCTGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (32 bp):
GTTTATTAAGCTTGGTTTATTTGAGAAACATC
Found at i:20792901 original size:18 final size:18
Alignment explanation
Indices: 20792846--20792904 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
20792836 TTATTGAGCT
*
20792846 TGGTTTATTTGAGAAGCA
1 TGGTTTATTTGAGAAACA
* *
20792864 TCGTTTA-TT---AAACT
1 TGGTTTATTTGAGAAACA
*
20792878 TAGTTTATTTGAGAAACA
1 TGGTTTATTTGAGAAACA
20792896 TGGTTTATT
1 TGGTTTATT
20792905 AAGCTTGGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
17 2 0.06
18 18 0.58
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.46
Consensus pattern (18 bp):
TGGTTTATTTGAGAAACA
Found at i:20801988 original size:22 final size:21
Alignment explanation
Indices: 20801960--20802015 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
20801950 TTTCGTAATA
*
20801960 AACTTATAATATA-CATATATTT
1 AACTTATAATA-AGCAT-TACTT
*
20801982 AATTTATACATAAGCATTACTT
1 AACTTATA-ATAAGCATTACTT
20802004 AACTTATAATAA
1 AACTTATAATAA
20802016 ACTTCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 19 0.66
23 6 0.21
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (21 bp):
AACTTATAATAAGCATTACTT
Found at i:20802556 original size:17 final size:18
Alignment explanation
Indices: 20802523--20802557 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20802513 TGACTATTTT
*
20802523 TTATTTAATATATAAATA
1 TTATTTAATAAATAAATA
20802541 TTATTTAA-AAATAAATA
1 TTATTTAATAAATAAATA
20802558 AATAACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTTAATAAATAAATA
Found at i:20803119 original size:23 final size:22
Alignment explanation
Indices: 20803066--20803119 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
20803056 GATCTTAAGG
*
20803066 TTTTTTCCTTATTCTTCTTTCT
1 TTTTTTCTTTATTCTTCTTTCT
*
20803088 TTTTCTCTTTATT-TTCTCTATCT
1 TTTTTTCTTTATTCTTCT-T-TCT
20803111 TTTTTTCTT
1 TTTTTTCTT
20803120 AATATTTAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 12 0.44
23 11 0.41
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTTCTTTATTCTTCTTTCT
Found at i:20806765 original size:28 final size:29
Alignment explanation
Indices: 20806723--20806783 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
20806713 GTAAATTTTT
* * *
20806723 AAAAATTACACTTTTGCCCCCATAAAGTG
1 AAAAATTACACTTTTGACCCCAAAAAATG
* *
20806752 AAAAATTATA-TTTTTACCCCAAAAAATG
1 AAAAATTACACTTTTGACCCCAAAAAATG
20806780 AAAA
1 AAAA
20806784 TTTGCCCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTGACCCCAAAAAATG
Found at i:20809114 original size:20 final size:20
Alignment explanation
Indices: 20809089--20809129 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20809079 ATAAGCTTTG
*
20809089 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
20809109 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
20809129 T
1 T
20809130 GAGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:20809145 original size:25 final size:25
Alignment explanation
Indices: 20809098--20809147 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20809088 GTTGATTTTT
*
20809098 ATGAAATGAAATTGATTTATATGAA
1 ATGAAATGAAATTGATGTATATGAA
*
20809123 ATGAAATGAGATTTGATGT-TATGAA
1 ATGAAATGA-AATTGATGTATATGAA
20809148 TCATATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (25 bp):
ATGAAATGAAATTGATGTATATGAA
Found at i:20813229 original size:19 final size:19
Alignment explanation
Indices: 20813205--20813242 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20813195 ACTTCTAAAC
20813205 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
20813224 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
20813243 ACAAATGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:20815506 original size:318 final size:314
Alignment explanation
Indices: 20814929--20815516 Score: 998
Period size: 318 Copynumber: 1.9 Consensus size: 314
20814919 TAGCACTCTA
* *
20814929 ATTCTTTGTTTTGGTAAGCATCATCTATAGACCAATGTAGAAAACTTTATTTTCCTTGTATCAAA
1 ATTCTTTGTTTTCGTAAGCATCATCTATAGACCAATGTAGAAAAATTTATTTTCCTTGTATCAAA
*
20814994 ATTAAGTCTAGTAATAAGAAATTTAACTTTTGGATTTTGTAAAAAAAAAAAAGTATTCCTCTTGT
66 ATTAAGTCTAGTAATAAGAAATTTAACTTTTAGATTTTGT---AAAAAAAAAGTATTCCTCTTGT
20815059 AATAAATTAATTAAATCTTTTTGGCCAATTTTTTCTTTACTTTAAGTAGACTGGGTAATTATTAT
128 AATAAATTAATTAAATCTTTTTGGCCAATTTTTTCTTTACTTTAAGTAGACTGGGTAATTATTAT
20815124 TACCTTCGAAATGATTTGCTAATACTAATAATATATTATTATCTTATATACCAACGGTGAAATTT
193 TACCTTCGAAATGATTTGCTAATACTAATAATATATTATTATCTTATATACCAACGGTGAAATTT
20815189 TTATGTTAAANTCTTTTCATTCATTCTTCATTTTTTAACCTGCCTTATTTGCACTATG
258 TTATGTTAAA-TCTTTTCATTCATTCTTCATTTTTTAACCTGCCTTATTTGCACTATG
* *
20815247 ATTCTTTGTTTTCGTAAGCTTCATCTATAGGCCAATGTAGAAAAATTTATTTTCCTTGTATCAAA
1 ATTCTTTGTTTTCGTAAGCATCATCTATAGACCAATGTAGAAAAATTTATTTTCCTTGTATC-AA
* * * * *
20815312 ATTTATTAAGTTTAGTAATAAGAAATTTAACTTTTAGTTTTTGT-ATAAAAAATTATTGCTCTTG
65 A---ATTAAGTCTAGTAATAAGAAATTTAACTTTTAGATTTTGTAAAAAAAAAGTATTCCTCTTG
*
20815376 TAATATATTAATTAAATCTTTTTGGCCAATTTTTTCTTTACTTTAAGTAGACTGGGTAATTATTA
127 TAATAAATTAATTAAATCTTTTTGGCCAATTTTTTCTTTACTTTAAGTAGACTGGGTAATTATTA
20815441 TTACCTTCGAAATGATTTGCTAATACTAATAATATATTATTATCTTATATACCAACGGTGAAATT
192 TTACCTTCGAAATGATTTGCTAATACTAATAATATATTATTATCTTATATACCAACGGTGAAATT
20815506 TTTATGTTAAA
257 TTTATGTTAAA
20815517 AGATATAGAT
Statistics
Matches: 255, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
318 215 0.84
319 3 0.01
322 37 0.15
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (314 bp):
ATTCTTTGTTTTCGTAAGCATCATCTATAGACCAATGTAGAAAAATTTATTTTCCTTGTATCAAA
ATTAAGTCTAGTAATAAGAAATTTAACTTTTAGATTTTGTAAAAAAAAAGTATTCCTCTTGTAAT
AAATTAATTAAATCTTTTTGGCCAATTTTTTCTTTACTTTAAGTAGACTGGGTAATTATTATTAC
CTTCGAAATGATTTGCTAATACTAATAATATATTATTATCTTATATACCAACGGTGAAATTTTTA
TGTTAAATCTTTTCATTCATTCTTCATTTTTTAACCTGCCTTATTTGCACTATG
Found at i:20816396 original size:2 final size:2
Alignment explanation
Indices: 20816391--20816415 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20816381 TATAACATTT
20816391 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20816416 TAATGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20823419 original size:110 final size:110
Alignment explanation
Indices: 20823221--20823440 Score: 368
Period size: 110 Copynumber: 2.0 Consensus size: 110
20823211 ATATGTTAGA
* ** * *
20823221 ATGGAATGTTTTTGTTAATATTTTTTATTGTAAACATGTGTGGGAATTAGTCTTGATTTTTACAT
1 ATGGAATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTACAT
*
20823286 TTTGATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCTTAT
66 TTTGATGATGATTTTGATAGTTTGTTTCAATTTCTTGTAGCTTAT
* *
20823331 ATGGCATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATAT
1 ATGGAATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTACAT
20823396 TTTGATGATGATTTTGATAGTTTGTTTCAATTTCTTGTAGCTTAT
66 TTTGATGATGATTTTGATAGTTTGTTTCAATTTCTTGTAGCTTAT
20823441 GTATAAATAT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (110 bp):
ATGGAATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTACAT
TTTGATGATGATTTTGATAGTTTGTTTCAATTTCTTGTAGCTTAT
Found at i:20826988 original size:14 final size:14
Alignment explanation
Indices: 20826969--20826998 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20826959 TACTATTTAA
*
20826969 TTTTAGTTTTAGTT
1 TTTTAGTTTTAATT
20826983 TTTTAGTTTTAATT
1 TTTTAGTTTTAATT
20826997 TT
1 TT
20826999 CCTTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (14 bp):
TTTTAGTTTTAATT
Found at i:20830105 original size:14 final size:14
Alignment explanation
Indices: 20830083--20830113 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20830073 CAACCACCCT
*
20830083 TGAATTTGAAAACA
1 TGAAGTTGAAAACA
20830097 TGAAGTTGAAAACA
1 TGAAGTTGAAAACA
20830111 TGA
1 TGA
20830114 GCATAAACTC
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:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (14 bp):
TGAAGTTGAAAACA
Found at i:20839490 original size:22 final size:22
Alignment explanation
Indices: 20839465--20839507 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20839455 CAAATACGAC
20839465 AATGAATCTTCGCTGCAGCGAG
1 AATGAATCTTCGCTGCAGCGAG
*
20839487 AATGAATTTTCGCTGCAGCGA
1 AATGAATCTTCGCTGCAGCGA
20839508 CGTTGGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
AATGAATCTTCGCTGCAGCGAG
Found at i:20845079 original size:2 final size:2
Alignment explanation
Indices: 20845067--20845097 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20845057 TGCAACAAGG
20845067 AT AT A- 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
20845098 GTTGGAGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20851643 original size:19 final size:19
Alignment explanation
Indices: 20851608--20851658 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
20851598 ATAATATTTT
20851608 AATATTATTTT-TTAATAA
1 AATATTATTTTATTAATAA
*
20851626 ATTATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
20851645 AATATTATTTTATT
1 AATATTATTTTATT
20851659 CTAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:20851665 original size:19 final size:18
Alignment explanation
Indices: 20851608--20851666 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
20851598 ATAATATTTT
20851608 AATATTA-TTT-TTTAATA
1 AATATTATTTTATTTAA-A
*
20851625 AATTATTATTTTATTAATAA
1 AA-TATTATTTTATTTA-AA
20851645 AATATTATTTTATTCTAAA
1 AATATTATTTTATT-TAAA
20851664 AAT
1 AAT
20851667 TTTCTCTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 20 0.57
20 7 0.20
21 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTATTTTATTTAAA
Found at i:20865945 original size:2 final size:2
Alignment explanation
Indices: 20865938--20865973 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20865928 TGCATAAGTG
*
20865938 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20865974 AAAACACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20866387 original size:2 final size:2
Alignment explanation
Indices: 20866380--20866439 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
20866370 NNNNNNTATC
* *
20866380 AT AT AT AT AT TT AG 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
20866422 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
20866440 CAACATAACA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20868670 original size:13 final size:13
Alignment explanation
Indices: 20868652--20868677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20868642 TTTCAAAAAA
20868652 TTTATAAAATCAT
1 TTTATAAAATCAT
20868665 TTTATAAAATCAT
1 TTTATAAAATCAT
20868678 AATTTCTTCT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20869924 original size:19 final size:19
Alignment explanation
Indices: 20869900--20869937 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20869890 ACTTCTAAAC
20869900 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
20869919 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
20869938 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:20871976 original size:11 final size:10
Alignment explanation
Indices: 20871957--20871982 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20871947 ATAAAACCCC
20871957 TTATTTTTTT
1 TTATTTTTTT
20871967 TTATTTTTTT
1 TTATTTTTTT
20871977 TTATTT
1 TTATTT
20871983 ATTTCTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:20872548 original size:16 final size:17
Alignment explanation
Indices: 20872519--20872551 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20872509 AATATCTAGA
*
20872519 AAATGTTTATATTATGT
1 AAATGTTTAAATTATGT
20872536 AAAT-TTTAAATTATGT
1 AAATGTTTAAATTATGT
20872552 CATGAATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
AAATGTTTAAATTATGT
Found at i:20877150 original size:11 final size:11
Alignment explanation
Indices: 20877134--20877167 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
20877124 TTAAACTGTG
20877134 AATGAAAAAGA
1 AATGAAAAAGA
20877145 AATGAAAAAGA
1 AATGAAAAAGA
*
20877156 AGAAGAAAAAGA
1 A-ATGAAAAAGA
20877168 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (11 bp):
AATGAAAAAGA
Found at i:20880297 original size:35 final size:35
Alignment explanation
Indices: 20880216--20880298 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
20880206 ACAAGGTCAC
* *
20880216 GCATAACCTTTATAACATGCCTTTTGCAAGATTAG
1 GCATAACCTCTATAACATGCCTTTTGCAAGATTAA
* *
20880251 GCGTAAACTCTATAACATGCCTTTTGC-AGAATTAA
1 GCATAACCTCTATAACATGCCTTTTGCAAG-ATTAA
*
20880286 GTATAACCTCTAT
1 GCATAACCTCTAT
20880299 CAAGACACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 2 0.05
35 38 0.95
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (35 bp):
GCATAACCTCTATAACATGCCTTTTGCAAGATTAA
Found at i:20886141 original size:17 final size:17
Alignment explanation
Indices: 20886111--20886143 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20886101 TTCTTGATAA
20886111 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
20886128 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
20886144 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:20886363 original size:59 final size:58
Alignment explanation
Indices: 20886299--20886456 Score: 192
Period size: 59 Copynumber: 2.7 Consensus size: 58
20886289 GTTTGTAATA
* * *
20886299 AAGACAAAAAATATTTTATCTTGTCTAAATTGAGACAAATATATTTTCTTGACTAAATT
1 AAGACAAAAAATAATTT-TCTTGTCTAAATTAAGACAAACATATTTTCTTGACTAAATT
* * * *
20886358 AAGACAAAAAAAAAATTTCTTGTCTTAAATTAAGGCAAACATATTTTCTTGTCTAAATT
1 AAGACAAAAAATAATTTTCTTGTC-TAAATTAAGACAAACATATTTTCTTGACTAAATT
* * * *
20886417 AAGACCAAACAT-GTTTTCCTGTCTAAATTAAGACAAACAT
1 AAGACAAAAAATAATTTTCTTGTCTAAATTAAGACAAACAT
20886457 GTCAAAGCTG
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
57 16 0.19
58 15 0.18
59 53 0.63
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (58 bp):
AAGACAAAAAATAATTTTCTTGTCTAAATTAAGACAAACATATTTTCTTGACTAAATT
Found at i:20886410 original size:29 final size:28
Alignment explanation
Indices: 20886299--20886456 Score: 163
Period size: 29 Copynumber: 5.4 Consensus size: 28
20886289 GTTTGTAATA
*
20886299 AAGACAAAAAATATTTTATCTTGTCTAAATT
1 AAGAC-AAACATA-TTT-TCTTGTCTAAATT
* * *
20886330 GAGACAAATATATTTTCTTGACTAAATT
1 AAGACAAACATATTTTCTTGTCTAAATT
* * *
20886358 AAGACAAAAAAAAAATTTCTTGTCTTAAATT
1 AAGAC--AAACATATTTTCTTGTC-TAAATT
*
20886389 AAGGCAAACATATTTTCTTGTCTAAATT
1 AAGACAAACATATTTTCTTGTCTAAATT
* *
20886417 AAGACCAAACATGTTTTCCTGTCTAAATT
1 AAGA-CAAACATATTTTCTTGTCTAAATT
20886446 AAGACAAACAT
1 AAGACAAACAT
20886457 GTCAAAGCTG
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
28 32 0.30
29 43 0.40
30 19 0.18
31 14 0.13
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (28 bp):
AAGACAAACATATTTTCTTGTCTAAATT
Found at i:20886467 original size:29 final size:29
Alignment explanation
Indices: 20886407--20886468 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
20886397 CATATTTTCT
***
20886407 TGTCTAAATTAAGACCAAACATGTTTTCC
1 TGTCTAAATTAAGACCAAACATGTAAACC
*
20886436 TGTCTAAATTAAGA-CAAACATGTCAAAGC
1 TGTCTAAATTAAGACCAAACATGT-AAACC
20886465 TGTC
1 TGTC
20886469 AATTTTGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (29 bp):
TGTCTAAATTAAGACCAAACATGTAAACC
Found at i:20893944 original size:33 final size:32
Alignment explanation
Indices: 20893894--20893956 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
20893884 TTAATTTACA
* *
20893894 AAAAAAATTAGATTATATAATAATAATTTTTT
1 AAAAAAATTAAAGTATATAATAATAATTTTTT
* *
20893926 AAAAAAATATAAAGTATATAATTATCATTTT
1 AAAAAAAT-TAAAGTATATAATAATAATTTT
20893957 AATATTGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (32 bp):
AAAAAAATTAAAGTATATAATAATAATTTTTT
Found at i:20894989 original size:30 final size:30
Alignment explanation
Indices: 20894947--20895011 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
20894937 ACGAATAAAA
*
20894947 TAAC-CATCCTCCCTAATCTTAATCTTCTT
1 TAACACATCCTCCCTAATCGTAATCTTCTT
*
20894976 TAACACATTCTCCCTAATCGTAATCTTCTT
1 TAACACATCCTCCCTAATCGTAATCTTCTT
*
20895006 CAACAC
1 TAACAC
20895012 TTTATTGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.28, C:0.34, G:0.02, T:0.37
Consensus pattern (30 bp):
TAACACATCCTCCCTAATCGTAATCTTCTT
Found at i:20895370 original size:23 final size:21
Alignment explanation
Indices: 20895356--20895397 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20895346 ATTTCAATAT
20895356 TTTA-AAAATAAATATTTTAA
1 TTTACAAAATAAATATTTTAA
*
20895376 TTTACAAAATAAATATTATAA
1 TTTACAAAATAAATATTTTAA
20895397 T
1 T
20895398 AAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTACAAAATAAATATTTTAA
Found at i:20901123 original size:33 final size:33
Alignment explanation
Indices: 20901086--20901153 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
20901076 TAAATACTTC
20901086 TATTTATTGATTTTATATAGGGTAAACTTCACA
1 TATTTATTGATTTTATATAGGGTAAACTTCACA
*
20901119 TATTTATTTATTTTATATAGGGTAAACTTCACA
1 TATTTATTGATTTTATATAGGGTAAACTTCACA
20901152 TA
1 TA
20901154 CACCCTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (33 bp):
TATTTATTGATTTTATATAGGGTAAACTTCACA
Found at i:20912170 original size:23 final size:23
Alignment explanation
Indices: 20912138--20912183 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20912128 TAAGGATTGT
*
20912138 CACCTGCTGAAACCACTAAAATA
1 CACCTACTGAAACCACTAAAATA
20912161 CACCTACTGAAACCACTAAAATA
1 CACCTACTGAAACCACTAAAATA
20912184 TTCCTTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.30, G:0.07, T:0.17
Consensus pattern (23 bp):
CACCTACTGAAACCACTAAAATA
Found at i:20920079 original size:2 final size:2
Alignment explanation
Indices: 20920072--20920107 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20920062 AACCCTACAG
20920072 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20920108 GCACTCTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20920141 original size:5 final size:5
Alignment explanation
Indices: 20920121--20920162 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
20920111 CTCTCCCAAG
*
20920121 TAAAA CTAAAA CAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
20920163 CAATATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 23 0.70
6 10 0.30
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:20920170 original size:10 final size:10
Alignment explanation
Indices: 20920122--20920170 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
20920112 TCTCCCAAGT
20920122 AAAACTAAAAC
1 AAAA-TAAAAC
*
20920133 AAAATAAAAT
1 AAAATAAAAC
*
20920143 AAAATAAAATA
1 AAAATAAAA-C
20920154 AAAATAAAAC
1 AAAATAAAAC
*
20920164 AATATAA
1 AAAATAA
20920171 TTAGAAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 20 0.61
11 13 0.39
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:20920170 original size:16 final size:16
Alignment explanation
Indices: 20920121--20920170 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
20920111 CTCTCCCAAG
*
20920121 TAAAACTAAAACAAAA
1 TAAAAATAAAACAAAA
*
20920137 T-AAAATAAAATAAAA
1 TAAAAATAAAACAAAA
*
20920152 TAAAAATAAAACAATA
1 TAAAAATAAAACAAAA
20920168 TAA
1 TAA
20920171 TTAGAAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
TAAAAATAAAACAAAA
Found at i:20924902 original size:39 final size:39
Alignment explanation
Indices: 20924859--20924937 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
20924849 CTATATAGCC
*
20924859 ATTACATCTTAACAAAGAATATAACATTTAATCATATCA
1 ATTACACCTTAACAAAGAATATAACATTTAATCATATCA
20924898 ATTACACCTTAACAAAGAATATAACATTTAATCATATCA
1 ATTACACCTTAACAAAGAATATAACATTTAATCATATCA
20924937 A
1 A
20924938 CATTTCATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (39 bp):
ATTACACCTTAACAAAGAATATAACATTTAATCATATCA
Found at i:20929160 original size:20 final size:20
Alignment explanation
Indices: 20929137--20929180 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
20929127 TAAATTTCAC
* *
20929137 AATCTATCAATACATTGCCA
1 AATCTATCAATAAATGGCCA
*
20929157 AATCTATTAATAAATGGCCA
1 AATCTATCAATAAATGGCCA
20929177 AATC
1 AATC
20929181 GATTACTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCTATCAATAAATGGCCA
Found at i:20962696 original size:32 final size:32
Alignment explanation
Indices: 20962654--20962737 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
20962644 ATGCAGAATA
20962654 TTGAA-GAAAAATTGGAAAAATTGG-AAATGTG
1 TTGAAGGAAAAA-TGGAAAAATTGGAAAATGTG
*
20962685 TTGAAGGAAAAATGGCAAAATTGGAAAATGTG
1 TTGAAGGAAAAATGGAAAAATTGGAAAATGTG
*
20962717 TTGAAGGAAAAA-AGAAAAATT
1 TTGAAGGAAAAATGGAAAAATT
20962738 CCTCATGAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
31 23 0.48
32 25 0.52
ACGTcount: A:0.51, C:0.01, G:0.25, T:0.23
Consensus pattern (32 bp):
TTGAAGGAAAAATGGAAAAATTGGAAAATGTG
Found at i:20964725 original size:43 final size:43
Alignment explanation
Indices: 20964560--20964712 Score: 227
Period size: 43 Copynumber: 3.6 Consensus size: 43
20964550 TTGACTCGAC
* *
20964560 TATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATTACCCGGT
1 TATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGATGACCCGGT
* *
20964603 TATATGTGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGGT
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGGT
* *
20964646 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGC
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGGT
*
20964689 CATGTGCGAGTAGGGAGTGCGCAT
1 TATGTGCGAGTAGGGAGTGCGCAT
20964713 GAGCTGGTGA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 1 0.01
43 99 0.99
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (43 bp):
TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGGT
Found at i:20964736 original size:20 final size:19
Alignment explanation
Indices: 20964711--20964773 Score: 90
Period size: 20 Copynumber: 3.2 Consensus size: 19
20964701 GGGAGTGCGC
20964711 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGA-GATGATG
20964731 ATGAGCTGGTGACGATGATG
1 ATGAGCTGGTGA-GATGATG
* *
20964751 ATGGGTTGGTGAGATGATG
1 ATGAGCTGGTGAGATGATG
20964770 ATGA
1 ATGA
20964774 TCATGGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 10 0.26
20 29 0.74
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.29
Consensus pattern (19 bp):
ATGAGCTGGTGAGATGATG
Found at i:20965613 original size:14 final size:13
Alignment explanation
Indices: 20965585--20965618 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
20965575 TTAACTTTGT
20965585 TGTTTAT-GTTTA
1 TGTTTATAGTTTA
20965597 TGTTTATAGTATTA
1 TGTTTATAGT-TTA
20965611 TGTTTATA
1 TGTTTATA
20965619 AAAATGGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 2 0.10
14 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TGTTTATAGTTTA
Found at i:20967581 original size:21 final size:20
Alignment explanation
Indices: 20967555--20967624 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
20967545 GGATATTTCT
20967555 TTTAAATTTAAACAGATTAAA
1 TTTAAATTTAAACA-ATTAAA
* ** *
20967576 TTTAAATATAATTAATCCT-TA
1 TTTAAATTTAAACAAT--TAAA
20967597 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAAC-AATTAAA
20967618 TTTAAAT
1 TTTAAAT
20967625 ATAATGGATT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 30 0.81
22 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (20 bp):
TTTAAATTTAAACAATTAAA
Found at i:20979255 original size:18 final size:18
Alignment explanation
Indices: 20979228--20979271 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20979218 ATATTTTTAT
*
20979228 TTAATCATGTTAAACATG
1 TTAATAATGTTAAACATG
*
20979246 TTAATAATGTTAAACGTG
1 TTAATAATGTTAAACATG
*
20979264 TTATTAAT
1 TTAATAAT
20979272 CGTGTCGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (18 bp):
TTAATAATGTTAAACATG
Found at i:20985938 original size:29 final size:30
Alignment explanation
Indices: 20985872--20985938 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
20985862 ATCTAAAAAG
*
20985872 AAGAATAAAAAAAAATTAATAAGGAATTATA
1 AAGAA-AAAAAAAAATTAAAAAGGAATTATA
* *
20985903 AATAAAAAATAAAA-TAAAAAGGAACTT-TA
1 AAGAAAAAAAAAAATTAAAAAGGAA-TTATA
20985932 AAGAAAA
1 AAGAAAA
20985939 CACAAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 17 0.55
30 10 0.32
31 4 0.13
ACGTcount: A:0.70, C:0.01, G:0.09, T:0.19
Consensus pattern (30 bp):
AAGAAAAAAAAAAATTAAAAAGGAATTATA
Found at i:20988923 original size:67 final size:67
Alignment explanation
Indices: 20988847--20988982 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 67
20988837 GAAAAGTTAG
*
20988847 TTTTGGGTTTTGGTTGATCTCAAGAAAAACCATTGTAAAAGGTTGTGGCTGAGCCTATGAAAACC
1 TTTTGGGTTTTGGTTGATCTCAAGAAAAACCATTGTAAAAGGTTGTGGCTAAGCCTATGAAAACC
20988912 CA
66 CA
** * * * *
20988914 TTTTGGGTTTTGGTTGATCTCGTGAAAAACCATTGTTAAAGGTTGTGGCTAAGCTTGTGAAAAGC
1 TTTTGGGTTTTGGTTGATCTCAAGAAAAACCATTGTAAAAGGTTGTGGCTAAGCCTATGAAAACC
20988979 CA
66 CA
20988981 TT
1 TT
20988983 GTAAAGGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCTCAAGAAAAACCATTGTAAAAGGTTGTGGCTAAGCCTATGAAAACC
CA
Found at i:20988975 original size:35 final size:35
Alignment explanation
Indices: 20988870--20988991 Score: 117
Period size: 35 Copynumber: 3.6 Consensus size: 35
20988860 TTGATCTCAA
* * *
20988870 GAAAAACCATTGTAAAAGGTTGTGGCTGAGCCTAT
1 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
* * * * * *
20988905 GAAAACCCATT-TT--GGGTTTTGGTTGATCTCGT
1 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
*
20988937 GAAAAACCATTGTTAAAGGTTGTGGCTAAGCTTGT
1 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
*
20988972 GAAAAGCCATTG-TAAAGGTT
1 GAAAAACCATTGTTAAAGGTT
20988992 TGGTGGAAGC
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
32 22 0.33
33 2 0.03
34 9 0.13
35 34 0.51
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (35 bp):
GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
Found at i:20989002 original size:34 final size:34
Alignment explanation
Indices: 20988935--20989004 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 34
20988925 GGTTGATCTC
20988935 GTGAAAAACCATTGTTAAAGGTTGTGGCTAAGCTT
1 GTGAAAAACCATTGTTAAAGGTTGTGGC-AAGCTT
*
20988970 GTGAAAAGCCATTG-TAAAGGTTTGGTGG-AAGCTT
1 GTGAAAAACCATTGTTAAAGG-TT-GTGGCAAGCTT
20989004 G
1 G
20989005 GGAATTCCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 13 0.41
35 15 0.47
36 4 0.12
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (34 bp):
GTGAAAAACCATTGTTAAAGGTTGTGGCAAGCTT
Found at i:20991193 original size:76 final size:77
Alignment explanation
Indices: 20991054--20991243 Score: 278
Period size: 76 Copynumber: 2.5 Consensus size: 77
20991044 AAAAGGTCAA
* * *
20991054 AAATTTTTTCCTACTTT-AGAGTAAATTTCTAAAATTAAGGATAGAATTTTAATTTTGGTTGATT
1 AAATTGTTTCCTACTTTAAAAG-AAATTCCTAAAATTAAGGATAGAATTTTAATTTTGGTTGATT
20991118 CATAAAGAATAGG
65 CATAAAGAATAGG
* *
20991131 AAATTGTTTCTTACTTTAAAA-AAATTCTTAAAATTAAGGATAGAATTTTAATTTTAGG-TGATT
1 AAATTGTTTCCTACTTTAAAAGAAATTCCTAAAATTAAGGATAGAATTTTAATTTT-GGTTGATT
*
20991194 CATAAAGAATATG
65 CATAAAGAATAGG
*
20991207 AAATTGTTTCCTATTTTAAAAGAAATTCCTAAAATTA
1 AAATTGTTTCCTACTTTAAAAGAAATTCCTAAAATTA
20991244 TGTGATAGCA
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
76 68 0.67
77 31 0.31
78 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (77 bp):
AAATTGTTTCCTACTTTAAAAGAAATTCCTAAAATTAAGGATAGAATTTTAATTTTGGTTGATTC
ATAAAGAATAGG
Found at i:20996549 original size:15 final size:15
Alignment explanation
Indices: 20996529--20996595 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 15
20996519 AAAGTAAGAA
20996529 GAGAAAGGAA-AAAAG
1 GAGAAA-GAAGAAAAG
*
20996544 GAGAAAGAAGAAAAA
1 GAGAAAGAAGAAAAG
20996559 GAGAAAGAA-AGAAAG
1 GAGAAAGAAGA-AAAG
20996574 GAGAAAGAAGAACAA-
1 GAGAAAGAAGAA-AAG
20996589 GAGAAAG
1 GAGAAAG
20996596 GAAGGTTCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.09
15 39 0.85
16 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.00
Consensus pattern (15 bp):
GAGAAAGAAGAAAAG
Found at i:20996561 original size:30 final size:31
Alignment explanation
Indices: 20996527--20996598 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 31
20996517 ACAAAGTAAG
20996527 AAGAGAAAGGAAA-AAAGGAGAAAGAAGAAA
1 AAGAGAAAGGAAAGAAAGGAGAAAGAAGAAA
*
20996557 AAGAGAAA-GAAAGAAAGGAGAAAGAAGAAC
1 AAGAGAAAGGAAAGAAAGGAGAAAGAAGAAA
20996587 AAGAGAAAGGAA
1 AAGAGAAAGGAA
20996599 GGTTCGGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 4 0.10
30 32 0.82
31 3 0.08
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (31 bp):
AAGAGAAAGGAAAGAAAGGAGAAAGAAGAAA
Found at i:21004604 original size:21 final size:21
Alignment explanation
Indices: 21004578--21004624 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21004568 AATATCAAGG
21004578 GTATCGATAGATTCCTTGCAT
1 GTATCGATAGATTCCTTGCAT
21004599 GTATCGATAGATTCCTTGCAT
1 GTATCGATAGATTCCTTGCAT
*
21004620 ATATC
1 GTATC
21004625 AATACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (21 bp):
GTATCGATAGATTCCTTGCAT
Found at i:21006867 original size:2 final size:2
Alignment explanation
Indices: 21006860--21006884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21006850 ACTTTCTATA
21006860 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
21006885 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21007727 original size:54 final size:54
Alignment explanation
Indices: 21007645--21007802 Score: 264
Period size: 54 Copynumber: 2.9 Consensus size: 54
21007635 TCATCCTGTG
21007645 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCATATAGCCGGACATCA
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCATATAGCCGGACATCA
* *
21007699 CATCTCACCTAGCTCATGTGCATCCCACCACATCGTGCATATAGCCGGACATCT
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCATATAGCCGGACATCA
* * *
21007753 CATCTCACCCAGCTCATGTGCAT-CCACCACATCGTGGACATAGCTGGACA
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCATATAGCCGGACA
21007803 GCATCACCAT
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 24 0.24
54 74 0.76
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCATATAGCCGGACATCA
Done.