Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 130 of 221
Found at i:40030972 original size:43 final size:43
Alignment explanation
Indices: 40030911--40030997 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
40030901 CATAGTTTGA
40030911 TTAGATTTATTGAATTCTACCAAGTTGGATACAGAAATTAATT
1 TTAGATTTATTGAATTCTACCAAGTTGGATACAGAAATTAATT
40030954 TTAGATTTATTGAATTCTACCAAGTTGGATACAGAAATTAATT
1 TTAGATTTATTGAATTCTACCAAGTTGGATACAGAAATTAATT
40030997 T
1 T
40030998 ATCTTATTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (43 bp):
TTAGATTTATTGAATTCTACCAAGTTGGATACAGAAATTAATT
Found at i:40031691 original size:19 final size:19
Alignment explanation
Indices: 40031662--40031707 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
40031652 GTTAAAGATG
*
40031662 TTATT-AAAATAAT-TTTTC
1 TTATTCAAAAT-ATGTTTTA
40031680 TTATTCAAAATATGTTTTA
1 TTATTCAAAATATGTTTTA
40031699 TTATTCAAA
1 TTATTCAAA
40031708 GTTATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATTCAAAATATGTTTTA
Found at i:40032009 original size:19 final size:20
Alignment explanation
Indices: 40031985--40032029 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
40031975 TCAAAAATTT
40031985 ATTTTAATATTT-TT-TATAC
1 ATTTTAAT-TTTATTATATAC
*
40032004 ATTTTAATTTTATTATGTAC
1 ATTTTAATTTTATTATATAC
40032024 ATTTTA
1 ATTTTA
40032030 TTACCTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTAATTTTATTATATAC
Found at i:40037290 original size:22 final size:21
Alignment explanation
Indices: 40037250--40037290 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40037240 AGTTTTAAGT
**
40037250 TTAGTTTTCTCTAGGTTTTCC
1 TTAGTTTTCTCTACATTTTCC
40037271 TTAGTTTTTCTCTACATTTT
1 TTAG-TTTTCTCTACATTTT
40037291 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (21 bp):
TTAGTTTTCTCTACATTTTCC
Found at i:40043976 original size:28 final size:27
Alignment explanation
Indices: 40043918--40043977 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
40043908 GAAGCATTTG
* **
40043918 TGGCAATCTATGAAATGAAAGTCTTTG
1 TGGCAATCTATGAAATGAAAGCCTTCA
* *
40043945 TGGCGATCTATGGAAATGAATGCCTTCA
1 TGGCAATCTAT-GAAATGAAAGCCTTCA
40043973 TGGCA
1 TGGCA
40043978 GATTCTAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (27 bp):
TGGCAATCTATGAAATGAAAGCCTTCA
Found at i:40044197 original size:27 final size:26
Alignment explanation
Indices: 40044141--40044258 Score: 94
Period size: 27 Copynumber: 4.4 Consensus size: 26
40044131 GCGTGTGGCT
* * * * *
40044141 AACTCTAAAGGACTGTAGATATGGTA
1 AACTCTGAAGGAATGAATATATGGTG
40044167 AACTCT-AAGAGAATGATATATATGGTG
1 AACTCTGAAG-GAATGA-ATATATGGTG
* *
40044194 AACTCTGAAGGAACAGAATATATGGCG
1 AACTCTGAAGGAA-TGAATATATGGTG
* ** *
40044221 AACTCTGAAGGAATAGCACGTATGGCG
1 AACTCTGAAGGAAT-GAATATATGGTG
40044248 AACTCTGAAGG
1 AACTCTGAAGG
40044259 GACGGTTCTA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
25 3 0.04
26 10 0.13
27 59 0.77
28 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (26 bp):
AACTCTGAAGGAATGAATATATGGTG
Found at i:40050782 original size:25 final size:25
Alignment explanation
Indices: 40050748--40050797 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40050738 TTAAACAACC
40050748 AACATACTTTCATCATGTCATATGT
1 AACATACTTTCATCATGTCATATGT
40050773 AACATACTTTCATCATGTCATATGT
1 AACATACTTTCATCATGTCATATGT
40050798 CAAACTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (25 bp):
AACATACTTTCATCATGTCATATGT
Found at i:40071515 original size:19 final size:19
Alignment explanation
Indices: 40071491--40071532 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40071481 TTTTTACTCT
*
40071491 TTTTGTT-TTTGTTTTACTA
1 TTTTGTTGTTT-TTTCACTA
40071510 TTTTGTTGTTTTTTCACTA
1 TTTTGTTGTTTTTTCACTA
40071529 TTTT
1 TTTT
40071533 ATTACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTGTTGTTTTTTCACTA
Found at i:40078354 original size:20 final size:20
Alignment explanation
Indices: 40078321--40078359 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40078311 TGAATTTTGT
*
40078321 AAAAATCAGAGTGAAATAGG
1 AAAAAACAGAGTGAAATAGG
* *
40078341 AAAAAACAGTGTGATATAG
1 AAAAAACAGAGTGAAATAG
40078360 TGAGCCAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAAAACAGAGTGAAATAGG
Found at i:40079441 original size:6 final size:6
Alignment explanation
Indices: 40079430--40079465 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
40079420 TGACATACCC
* *
40079430 CTAAAG CTAAAG CTGAAG CTAAAG CTGAAG CTAAAG
1 CTAAAG CTAAAG CTAAAG CTAAAG CTAAAG CTAAAG
40079466 TCAAGCAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (6 bp):
CTAAAG
Found at i:40079450 original size:12 final size:12
Alignment explanation
Indices: 40079433--40079465 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40079423 CATACCCCTA
40079433 AAGCTAAAGCTG
1 AAGCTAAAGCTG
40079445 AAGCTAAAGCTG
1 AAGCTAAAGCTG
40079457 AAGCTAAAG
1 AAGCTAAAG
40079466 TCAAGCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (12 bp):
AAGCTAAAGCTG
Found at i:40082111 original size:15 final size:15
Alignment explanation
Indices: 40082091--40082120 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40082081 CACTTTTCCA
40082091 TTTTATGCATAATAT
1 TTTTATGCATAATAT
40082106 TTTTATGCATAATAT
1 TTTTATGCATAATAT
40082121 CCCACTCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTATGCATAATAT
Found at i:40084049 original size:3 final size:3
Alignment explanation
Indices: 40084041--40084098 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
40084031 CCACTTAAGA
*
40084041 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40084089 AA- AAG AAG AA
1 AAG AAG AAG AA
40084099 CCTTCTTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:40084169 original size:3 final size:3
Alignment explanation
Indices: 40084161--40084245 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
40084151 CAATTTAACA
40084161 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40084209 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
40084246 CCTGCTTCAG
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40103069 original size:20 final size:20
Alignment explanation
Indices: 40103044--40103084 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40103034 CACATGGTAG
*
40103044 TGTGTTTGAAAACCATAACT
1 TGTGTTGGAAAACCATAACT
*
40103064 TGTGTTGGGAAACCATAACT
1 TGTGTTGGAAAACCATAACT
40103084 T
1 T
40103085 TACTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTGTTGGAAAACCATAACT
Found at i:40145273 original size:29 final size:29
Alignment explanation
Indices: 40145241--40145315 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
40145231 TTTTTTTTAA
*
40145241 ATTTACCGAAATGGGTCAGGTATTTTATT
1 ATTTACCGAAATGGGCCAGGTATTTTATT
*
40145270 ATTTACTGAAATGGGCCAGGTATTTTATT
1 ATTTACCGAAATGGGCCAGGTATTTTATT
40145299 ATTTACC-AGAATGGGCC
1 ATTTACCGA-AATGGGCC
40145316 CTTTTCCCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (29 bp):
ATTTACCGAAATGGGCCAGGTATTTTATT
Found at i:40145600 original size:12 final size:12
Alignment explanation
Indices: 40145583--40145635 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
40145573 ACTAATACTC
40145583 TCTCAAATTTCT
1 TCTCAAATTTCT
40145595 TCTC-AATTTGCT
1 TCTCAAATTT-CT
*
40145607 T-TCAAATTCCT
1 TCTCAAATTTCT
*
40145618 TC-AAAATTTC-
1 TCTCAAATTTCT
40145628 TCTCAAAT
1 TCTCAAAT
40145636 CCATATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
10 2 0.06
11 20 0.61
12 11 0.33
ACGTcount: A:0.28, C:0.25, G:0.02, T:0.45
Consensus pattern (12 bp):
TCTCAAATTTCT
Found at i:40145625 original size:23 final size:22
Alignment explanation
Indices: 40145581--40145635 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
40145571 AAACTAATAC
* **
40145581 TCTCTCAAATTTCTTCTCAATT
1 TCTCTCAAATTCCTTCAAAATT
*
40145603 TGCTTTCAAATTCCTTCAAAATT
1 T-CTCTCAAATTCCTTCAAAATT
40145626 TCTCTCAAAT
1 TCTCTCAAAT
40145636 CCATATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (22 bp):
TCTCTCAAATTCCTTCAAAATT
Found at i:40145657 original size:51 final size:51
Alignment explanation
Indices: 40145597--40145694 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
40145587 AAATTTCTTC
*
40145597 TCAATTTGCTTTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTGT-AAAATTTCTCTCAAATCCATATTTATTT
* * * *
40145648 TCAATTTGCTCTCAAGTTCCTGTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCCTGTAAAATTTCTCTCAAATCCATATTT
40145695 TTAAATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTGTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:40147496 original size:18 final size:18
Alignment explanation
Indices: 40147473--40147512 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40147463 CAGGTGCGTT
*
40147473 TCCTAACCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
40147491 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
40147509 TCCT
1 TCCT
40147513 TTTTCCAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:40147810 original size:21 final size:21
Alignment explanation
Indices: 40147770--40147816 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40147760 ATGCCCTATT
*
40147770 GGAAGAACCAGAATCCCCGCC
1 GGAAGAACCACAATCCCCGCC
40147791 GGAAGAACCACAA-CCGCCGCC
1 GGAAGAACCACAATCC-CCGCC
*
40147812 AGAAG
1 GGAAG
40147817 CTGGACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.36, C:0.36, G:0.26, T:0.02
Consensus pattern (21 bp):
GGAAGAACCACAATCCCCGCC
Found at i:40148132 original size:22 final size:22
Alignment explanation
Indices: 40148107--40148208 Score: 145
Period size: 22 Copynumber: 4.7 Consensus size: 22
40148097 CTTAAATTAA
*
40148107 AAACCCTTAACCTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
40148129 AAACCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
* *
40148151 -AACCCTTAACTTTAAAATCCT
1 AAACCCTTAACTTAAAAACCCT
* *
40148172 AAACCCTTAAATTTAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
40148194 -AACCCTTAACTTAAA
1 AAACCCTTAACTTAAA
40148209 TATAATTTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
21 32 0.44
22 40 0.56
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACCCTTAACTTAAAAACCCT
Found at i:40148133 original size:15 final size:15
Alignment explanation
Indices: 40148104--40148133 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40148094 ACCCTTAAAT
*
40148104 TAAAAACCCTTAACC
1 TAAAAACCCTAAACC
40148119 TAAAAACCCTAAACC
1 TAAAAACCCTAAACC
40148134 CTTAACTTAA
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:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAACCCTAAACC
Found at i:40148148 original size:15 final size:15
Alignment explanation
Indices: 40148065--40148128 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 15
40148055 GACAAACCTT
40148065 AAACCCTTAACTTAA
1 AAACCCTTAACTTAA
*
40148080 AAACCC-TAAC--CA
1 AAACCCTTAACTTAA
** *
40148092 TGACCCTTAAATTAA
1 AAACCCTTAACTTAA
*
40148107 AAACCCTTAACCTAA
1 AAACCCTTAACTTAA
40148122 AAACCCT
1 AAACCCT
40148129 AAACCCTTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
12 5 0.14
13 3 0.08
14 4 0.11
15 25 0.68
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (15 bp):
AAACCCTTAACTTAA
Found at i:40148166 original size:64 final size:65
Alignment explanation
Indices: 40148058--40148208 Score: 189
Period size: 64 Copynumber: 2.4 Consensus size: 65
40148048 TTTAATTGAC
* * * *
40148058 AAACCTTAAACCCTTAACTTAAAAACCCTAACCATGACCCTT-AAATTAAAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCATGAACCTTAAAATCAAAAACCCTTAAACTAA
* * * ** * *
40148122 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAATCCTAAACCCTTAAATTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCATGAACCTTAAAATCAAAAACCCTTAAACTAA
40148187 AAACCCT-AACCCTTAACTTAAA
1 AAACCCTAAACCCTTAACTTAAA
40148209 TATAATTTGA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
64 52 0.69
65 23 0.31
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.25
Consensus pattern (65 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAACCATGAACCTTAAAATCAAAAACCCTTAAACTAA
Found at i:40148173 original size:43 final size:43
Alignment explanation
Indices: 40148108--40148208 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
40148098 TTAAATTAAA
* *
40148108 AACCCTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAAATTAAAAACCCT
* * *
40148151 AACCCTTAACTTTAAAATCCTAAACCCTTAAATTTAAAACCCT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAAATTAAAAACCCT
40148194 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
40148209 TATAATTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (43 bp):
AACCCTTAACTTAAAAACCCTAAACCCTTAAATTAAAAACCCT
Found at i:40151515 original size:124 final size:124
Alignment explanation
Indices: 40151355--40151919 Score: 622
Period size: 125 Copynumber: 4.5 Consensus size: 124
40151345 CCTAAACATG
* * * *
40151355 CTACTGTAGAAAAAGCGCGTTCAAGTA-GGCGCGATTTCACAAATTCTTCTCATAAAGCATCTTG
1 CTACTGTAGCAAAAGCGCGTCCACG-AGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
* * * *
40151419 CTAGAAGCGATTTTATACTATTTGCTCAGAAATG-CTAAGTCGAAATTATTTTTCCAAGAC
65 CTTGAAGCGATTTTAAACTATTTGCTCAGAAACGTC-AACTCGAAATTATTTTTCCAAGAC
* *
40151479 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAACATGCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * * *
40151543 CTTGCAGCGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTA-TTTT-CAGGAC
65 CTTGAAGCG--ATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* ** * * * *
40151603 CTACTATAGCAAAAATGCATCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
** *
40151668 TTGAAGCTTTTTTAAAACTATTTGCTCA-AAAAGTCAACTCGAAATTATTTCTTCCAAGAC
66 TTGAAGCGATTTT-AAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAAGAC
* * * *
40151728 CAACTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTTC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
40151793 TTGAAGC-ATTTTTTAAACTTTTTGATCAGAAACGTCAAGTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGA--TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* * * * * * * * *
40151853 CTACTGTAGCAAAAGTGCGTACATGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
40151918 TT
66 TT
40151920 TGATTTTATC
Statistics
Matches: 369, Mismatches: 59, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
122 21 0.06
123 18 0.05
124 126 0.34
125 146 0.40
126 57 0.15
127 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
Found at i:40162349 original size:4 final size:4
Alignment explanation
Indices: 40162340--40162372 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
40162330 TATCCTCCCC
40162340 CCCA CCCA CCCA CCCA CCCA CCCA CCCA CCCA C
1 CCCA CCCA CCCA CCCA CCCA CCCA CCCA CCCA C
40162373 TCAAACTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.76, G:0.00, T:0.00
Consensus pattern (4 bp):
CCCA
Found at i:40165377 original size:16 final size:15
Alignment explanation
Indices: 40165356--40165395 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
40165346 TTTATGCTTG
40165356 TGAAAAAAATGAAAAA
1 TGAAAAAAA-GAAAAA
*
40165372 TGAAAAGAAAGAGAAA
1 TGAAAA-AAAGAAAAA
40165388 TGAAAAAA
1 TGAAAAAA
40165396 TGGATTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 17 0.77
17 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (15 bp):
TGAAAAAAAGAAAAA
Found at i:40167278 original size:27 final size:27
Alignment explanation
Indices: 40167247--40167320 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 27
40167237 GTTCATTGGC
40167247 CTAGTTTAGATTTAGTGGTTGTGAGGT
1 CTAGTTTAGATTTAGTGGTTGTGAGGT
* * * *
40167274 CTAGTTTACATAGTGTATTAGTTTTGAGGT
1 CTAGTTTAGAT--T-TAGTGGTTGTGAGGT
*
40167304 CTATTTTAGATTTAGTG
1 CTAGTTTAGATTTAGTG
40167321 ACCTAGTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
27 13 0.36
28 1 0.03
29 1 0.03
30 21 0.58
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (27 bp):
CTAGTTTAGATTTAGTGGTTGTGAGGT
Found at i:40168997 original size:12 final size:12
Alignment explanation
Indices: 40168980--40169008 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40168970 AAGCTTTTTC
40168980 TTTTAGAAGCTG
1 TTTTAGAAGCTG
40168992 TTTTAGAAGCTG
1 TTTTAGAAGCTG
40169004 TTTTA
1 TTTTA
40169009 ACAATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (12 bp):
TTTTAGAAGCTG
Found at i:40169019 original size:23 final size:23
Alignment explanation
Indices: 40168992--40169043 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
40168982 TTAGAAGCTG
*
40168992 TTTTAGAAGCTGTTTTAACAATC
1 TTTTAGAAGCTGTTTTAACAATA
*
40169015 TTTTAGAAGTTGTTTTAACAATA
1 TTTTAGAAGCTGTTTTAACAATA
40169038 TTTTAG
1 TTTTAG
40169044 GTTGTGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTTAGAAGCTGTTTTAACAATA
Found at i:40171904 original size:30 final size:30
Alignment explanation
Indices: 40171870--40171929 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40171860 AGAGTATACA
40171870 ATAAGAAGCTTTGAATCATGGTACTACTTG
1 ATAAGAAGCTTTGAATCATGGTACTACTTG
40171900 ATAAGAAGCTTTGAATCATGGTACTACTTG
1 ATAAGAAGCTTTGAATCATGGTACTACTTG
40171930 TGGACCGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (30 bp):
ATAAGAAGCTTTGAATCATGGTACTACTTG
Found at i:40172654 original size:17 final size:17
Alignment explanation
Indices: 40172634--40172672 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40172624 CCAAAAATAA
40172634 TAATATTTTAA-TAAATT
1 TAATA-TTTAATTAAATT
*
40172651 TAATATTTAATTTAATT
1 TAATATTTAATTAAATT
40172668 TAATA
1 TAATA
40172673 CTTATCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATATTTAATTAAATT
Found at i:40182083 original size:6 final size:6
Alignment explanation
Indices: 40182072--40182127 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
40182062 TTCTTATTTC
* *
40182072 AAAAAT AAAAAT -AAAAT AAAAAT AACACT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
40182119 AAAAAT AAA
1 AAAAAT AAA
40182128 GAAGACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40200185 original size:16 final size:16
Alignment explanation
Indices: 40200164--40200195 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40200154 GTTTTGTTGC
*
40200164 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
40200180 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
40200196 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:40200567 original size:50 final size:49
Alignment explanation
Indices: 40200419--40200610 Score: 210
Period size: 50 Copynumber: 3.8 Consensus size: 49
40200409 GATACCGGTT
* * *
40200419 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATATGACCATCA-T-TCTGGTA
* * *
40200470 CACGTAGTAGCCTGCACATAGTACCACACACGTGATTGA--AGCA-TCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACA--T-A-TGACCATCATTCTGGTA
* * *
40200520 CGCATAGTAGCTTGCACATAGTACTACACATACGACCTATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATATGACC-ATCATTCTGGTA
*
40200570 CACGTAGTAGCCTGCACATAGTACTACACATATGACCATCA
1 CACATAGTAGCCTGCACATAGTACTACACATATGACCATCA
40200611 CTTTCACTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
46 2 0.02
47 1 0.01
48 1 0.01
49 7 0.06
50 71 0.61
51 28 0.24
53 4 0.03
55 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACATATGACCATCATTCTGGTA
Found at i:40200628 original size:101 final size:100
Alignment explanation
Indices: 40200416--40200599 Score: 246
Period size: 101 Copynumber: 1.8 Consensus size: 100
40200406 AATGATACCG
**
40200416 GTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATACGACCATCACTATCCGATACACGTAGTAGC
**
40200481 CTGCACATAGTACCACACACGTGATTGAAGCATCTG
66 CTGCACATAGTACCACACAC-TGATTGAAGCATCAC
* * * * *
40200517 GTACGCATAGTAGCTTGCACATAGTACTACACATACGACCTATCA-T-TCTGGTACACGTAGTAG
1 GTTCACATAGTAGCCTGCACATAGTACTACACATACGACC-ATCACTATCCGATACACGTAGTAG
*
40200580 CCTGCACATAGTACTACACA
65 CCTGCACATAGTACCACACA
40200600 TATGACCATC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 34 0.46
101 36 0.49
102 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (100 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATACGACCATCACTATCCGATACACGTAGTAGC
CTGCACATAGTACCACACACTGATTGAAGCATCAC
Found at i:40202697 original size:16 final size:17
Alignment explanation
Indices: 40202676--40202709 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40202666 TTGGATTGAG
40202676 AAAATT-ATTTAATTAA
1 AAAATTAATTTAATTAA
*
40202692 AAAATTAATTTATTTAA
1 AAAATTAATTTAATTAA
40202709 A
1 A
40202710 TTATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:40205298 original size:42 final size:43
Alignment explanation
Indices: 40205093--40205288 Score: 252
Period size: 43 Copynumber: 4.6 Consensus size: 43
40205083 TTTGCGACGC
40205093 CTTTTC-CACAAACGCCGCTATAAACCACGACCTTTAGCGGCA
1 CTTTTCTCACAAACGCCGCTATAAACCACGACCTTTAGCGGCA
* *
40205135 CTTTTCTCACAAACGCCGCTATAGACCATGACCTTTAGCGGCA
1 CTTTTCTCACAAACGCCGCTATAAACCACGACCTTTAGCGGCA
* ** *
40205178 CTTTTCCCACAAACGCCGCTATTGACCACGACCTTTAGCGGCG
1 CTTTTCTCACAAACGCCGCTATAAACCACGACCTTTAGCGGCA
* * * *
40205221 CTTTTATCACAAACGCCGCTAAAAAACA-AACCTTTAGCGGCA
1 CTTTTCTCACAAACGCCGCTATAAACCACGACCTTTAGCGGCA
* * * *
40205263 CTTCTCGCAAAAACGCCGCTAAAAAC
1 CTTTTCTCACAAACGCCGCTATAAAC
40205289 ATAACCTTTA
Statistics
Matches: 134, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
42 39 0.29
43 95 0.71
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.22
Consensus pattern (43 bp):
CTTTTCTCACAAACGCCGCTATAAACCACGACCTTTAGCGGCA
Found at i:40207212 original size:22 final size:22
Alignment explanation
Indices: 40207184--40207227 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40207174 CAACGTTATA
40207184 TAAAATTCTTATAGCCAATAGC
1 TAAAATTCTTATAGCCAATAGC
40207206 TAAAATTCTTATAGCCAATAGC
1 TAAAATTCTTATAGCCAATAGC
40207228 CAATATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
TAAAATTCTTATAGCCAATAGC
Found at i:40209992 original size:146 final size:147
Alignment explanation
Indices: 40209727--40210020 Score: 450
Period size: 146 Copynumber: 2.0 Consensus size: 147
40209717 GGGGGATTTT
*
40209727 TATAAAATGGCGCTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTATAAAACGCCGC
1 TATAAAATGGCACTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTATAAAACGCCGC
* * *** *
40209792 TATTTCTTACATTTTGCGATGTTTTTGTGAAAAACGCTGTAACAAATTATTTCATTTGGAATAAA
66 TATTGCTTACATTTTGCGATGTTTTTATGAAAAACGCCACAAAAAATTATTTCATTTGGAATAAA
*
40209857 ATGACACTGTTTTGCTA
131 ACGACACTGTTTTGCTA
*
40209874 TATAAAATGGCACTA-TTTTTTTAAAGTAAAATTATTTTTTGTGGCG-TTTTTATAAAAACGCCG
1 TATAAAATGGCACTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTAT-AAAACGCCG
* *
40209937 CTATTGCTTACCTTTTGCGGTGTTTTTCAT-AAAAACGCCACAAAAAATTATTTCATTTGGAATA
65 CTATTGCTTACATTTTGCGATGTTTTT-ATGAAAAACGCCACAAAAAATTATTTCATTTGGAATA
40210001 AAACGACACTGTTTTGCTA
129 AAACGACACTGTTTTGCTA
40210020 T
1 T
40210021 GCTTAAAATC
Statistics
Matches: 134, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
145 7 0.05
146 112 0.84
147 15 0.11
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (147 bp):
TATAAAATGGCACTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTATAAAACGCCGC
TATTGCTTACATTTTGCGATGTTTTTATGAAAAACGCCACAAAAAATTATTTCATTTGGAATAAA
ACGACACTGTTTTGCTA
Found at i:40210843 original size:7 final size:7
Alignment explanation
Indices: 40210831--40210875 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
40210821 ACTATCTCTT
40210831 AACCCCA
1 AACCCCA
40210838 AACCCCA
1 AACCCCA
40210845 AACCCCA
1 AACCCCA
40210852 AACCCCA
1 AACCCCA
40210859 AACCCCA
1 AACCCCA
40210866 AACCCCA
1 AACCCCA
40210873 AAC
1 AAC
40210876 TCCTAGCCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:40211150 original size:14 final size:15
Alignment explanation
Indices: 40211133--40211165 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40211123 CTTAAATCAG
*
40211133 AATCCCTGA-TCCAT
1 AATCCCTAATTCCAT
40211147 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
40211162 AATC
1 AATC
40211166 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:40211640 original size:41 final size:40
Alignment explanation
Indices: 40211583--40211735 Score: 164
Period size: 41 Copynumber: 3.8 Consensus size: 40
40211573 CGCTTTTTCA
* *
40211583 AAAACGCCGCTAAAGCCCCGAGCATTAGCGACACATCTTGG
1 AAAACGCCGCTAAAGCCCAGAGCATTAGCGGCAC-TCTTGG
* **
40211624 AAAACGCCGCTAAAG-CCAGAGCATTAGCGGCACTTTTCCA
1 AAAACGCCGCTAAAGCCCAGAGCATTAGCGGCACTCTT-GG
** * *
40211664 AAAACGCCGCTAAAGATCTGAGCATTAGCGGCTCTTCTTGG
1 AAAACGCCGCTAAAGCCCAGAGCATTAGCGGCAC-TCTTGG
* * *
40211705 AAAACACCACTAAATCCCAGAGCATTAGCGG
1 AAAACGCCGCTAAAGCCCAGAGCATTAGCGG
40211736 TGCTTTTCCA
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 31 0.34
41 55 0.60
42 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.18
Consensus pattern (40 bp):
AAAACGCCGCTAAAGCCCAGAGCATTAGCGGCACTCTTGG
Found at i:40211704 original size:81 final size:82
Alignment explanation
Indices: 40211569--40211769 Score: 269
Period size: 81 Copynumber: 2.5 Consensus size: 82
40211559 AAATGTTTTT
* ** * * *
40211569 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGACACATCTTGGAAAACGCCGC
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGACACATCTTGGAAAACACCAC
*
40211634 TAAA-GCCAGAGCATTA
66 TAAATCCCAGAGCATTA
* * * *
40211650 GCGGCACTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCTCTTCTTGGAAAACACCAC
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGACACATCTTGGAAAACACCAC
40211715 TAAATCCCAGAGCATTA
66 TAAATCCCAGAGCATTA
* * *
40211732 GCGGTGCTTTTCCAAAAATGCCACTAAAGATCTGAGCA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCA
40211770 AATCTGAGCA
Statistics
Matches: 104, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 59 0.57
82 45 0.43
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (82 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGACACATCTTGGAAAACACCAC
TAAATCCCAGAGCATTA
Found at i:40211756 original size:41 final size:39
Alignment explanation
Indices: 40211624--40211761 Score: 109
Period size: 41 Copynumber: 3.4 Consensus size: 39
40211614 CACATCTTGG
* * *
40211624 AAAACGCCGCTAAAG-CCAGAGCATTAGCGGCACTTTTCC
1 AAAAAGCCACTAAAGACCAGAGCATTAGCGG-TCTTTTCC
* * * **
40211663 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCTCTTCTTGG
1 AAAAA-GCCACTAAAGACCAGAGCATTAGCGG-TCTT-TTCC
**
40211705 AAAACA-CCACTAAATCCCAGAGCATTAGCGGTGCTTTTCC
1 AAAA-AGCCACTAAAGACCAGAGCATTAGCGGT-CTTTTCC
40211745 AAAAATGCCACTAAAGA
1 AAAAA-GCCACTAAAGA
40211762 TCTGAGCAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
39 5 0.06
40 17 0.22
41 48 0.62
42 6 0.08
43 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (39 bp):
AAAAAGCCACTAAAGACCAGAGCATTAGCGGTCTTTTCC
Found at i:40211769 original size:41 final size:39
Alignment explanation
Indices: 40211642--40211769 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 39
40211632 GCTAAAGCCA
* *
40211642 GAGCATTAGCGGCACTTTTCCAAAAACGCCGCTAAAGATCT
1 GAGCATTAGCGG-TCTTTTCCAAAAA-GCCACTAAAGATCT
** *** *
40211683 GAGCATTAGCGGCTCTTCTTGGAAAACA-CCACTAAATCCCA
1 GAGCATTAGCGG-TCTT-TTCCAAAA-AGCCACTAAAGATCT
40211724 GAGCATTAGCGGTGCTTTTCCAAAAATGCCACTAAAGATCT
1 GAGCATTAGCGGT-CTTTTCCAAAAA-GCCACTAAAGATCT
40211765 GAGCA
1 GAGCA
40211770 AATCTGAGCA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 7 0.10
41 53 0.78
42 6 0.09
43 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (39 bp):
GAGCATTAGCGGTCTTTTCCAAAAAGCCACTAAAGATCT
Found at i:40221385 original size:27 final size:27
Alignment explanation
Indices: 40221355--40221416 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
40221345 TATAAAATAA
* * *
40221355 TTAAAATTCAATTTTTTTA-AATGAAGG
1 TTAAAATT-AATTATTTTATAATAAAAG
40221382 TT-AAATTAATTATTTTATAATAAAAG
1 TTAAAATTAATTATTTTATAATAAAAG
40221408 TATAAAATT
1 T-TAAAATT
40221417 TGACAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 9 0.31
26 12 0.41
27 3 0.10
28 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (27 bp):
TTAAAATTAATTATTTTATAATAAAAG
Found at i:40224716 original size:43 final size:43
Alignment explanation
Indices: 40224665--40224758 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
40224655 GAGTCCTCAG
* * * *
40224665 TGCATCATCAGATAAACCGAAGCAAATATATTGGCACACATAA
1 TGCATCATCAAACAAACCGAAGCAAATATACTGACACACATAA
* *
40224708 TGTATCATCAAACAAACCGAAGCAAATATACTGACACACATAG
1 TGCATCATCAAACAAACCGAAGCAAATATACTGACACACATAA
40224751 TGCATCAT
1 TGCATCAT
40224759 TGGAAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.21
Consensus pattern (43 bp):
TGCATCATCAAACAAACCGAAGCAAATATACTGACACACATAA
Found at i:40225338 original size:9 final size:9
Alignment explanation
Indices: 40225324--40225350 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40225314 TACATCCAAG
40225324 TTTAATTTA
1 TTTAATTTA
40225333 TTTAATTTA
1 TTTAATTTA
40225342 TTTAATTTA
1 TTTAATTTA
40225351 GTCCCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTAATTTA
Found at i:40235457 original size:46 final size:44
Alignment explanation
Indices: 40235440--40235664 Score: 185
Period size: 46 Copynumber: 5.3 Consensus size: 44
40235430 GACAAGTGGA
* * * * *
40235440 AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATA
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGA-C
* * *
40235486 AAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
40235531 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 -AAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAGAGAC
*
40235577 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
40235614 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGGGAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
40235651 AAGTGATAAGTGAT
1 AAGTGATAAGTGAT
40235665 CATACGTAAG
Statistics
Matches: 165, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
36 9 0.05
37 58 0.35
38 1 0.01
39 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 91 0.55
47 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (44 bp):
AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
Found at i:40235458 original size:52 final size:48
Alignment explanation
Indices: 40235373--40235589 Score: 234
Period size: 46 Copynumber: 4.6 Consensus size: 48
40235363 TTTGAGTACT
* * *
40235373 TCTGATCAAGTG--ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
40235419 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGAC-A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
40235471 TCTGATCAAGTG--ATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
40235517 TCTGATCAAGAGAC--AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40235563 TCTGATCAAGAGAC--AAAGTGATAAGTG
1 TCTGATCAAGAGACATAAAGTGATAAGTG
40235590 GCTACACTTA
Statistics
Matches: 152, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
46 109 0.72
48 1 0.01
49 2 0.01
50 1 0.01
52 39 0.26
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (48 bp):
TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:40235597 original size:37 final size:37
Alignment explanation
Indices: 40235553--40235662 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
40235543 GATAGCTTTA
40235553 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40235590 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40235627 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
40235663 ATCATACGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:40236983 original size:49 final size:49
Alignment explanation
Indices: 40236917--40237060 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
40236907 ATGTGAACAT
40236917 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
40236967 GTGATATGTGACTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
40237016 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
40237061 AGAAAATGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 83 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:40240273 original size:46 final size:44
Alignment explanation
Indices: 40240256--40240480 Score: 185
Period size: 46 Copynumber: 5.3 Consensus size: 44
40240246 GACAAGTGGA
* * * * *
40240256 AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATA
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGA-C
* * *
40240302 AAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
40240347 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 -AAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAGAGAC
*
40240393 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
40240430 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGGGAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
40240467 AAGTGATAAGTGAT
1 AAGTGATAAGTGAT
40240481 CATACGTAAG
Statistics
Matches: 165, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
36 9 0.05
37 58 0.35
38 1 0.01
39 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 91 0.55
47 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (44 bp):
AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
Found at i:40240274 original size:52 final size:48
Alignment explanation
Indices: 40240189--40240405 Score: 234
Period size: 46 Copynumber: 4.6 Consensus size: 48
40240179 TTTGAGTACT
* * *
40240189 TCTGATCAAGTG--ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
40240235 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGAC-A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
40240287 TCTGATCAAGTG--ATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
40240333 TCTGATCAAGAGAC--AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40240379 TCTGATCAAGAGAC--AAAGTGATAAGTG
1 TCTGATCAAGAGACATAAAGTGATAAGTG
40240406 GCTACACTTA
Statistics
Matches: 152, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
46 109 0.72
48 1 0.01
49 2 0.01
50 1 0.01
52 39 0.26
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (48 bp):
TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:40240413 original size:37 final size:37
Alignment explanation
Indices: 40240369--40240478 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
40240359 GATAGCTTTA
40240369 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40240406 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40240443 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
40240479 ATCATACGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:40242312 original size:6 final size:6
Alignment explanation
Indices: 40242301--40242359 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
40242291 AGGAGGAAGA
* ** *
40242301 AAAATC AAAATC AAAATC AAAAGC AAAAAGA AAAATC AAAATC AAAGTC
1 AAAATC AAAATC AAAATC AAAATC -AAAATC AAAATC AAAATC AAAATC
*
40242350 AAAGTC AAAA
1 AAAATC AAAA
40242360 AATGAAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 41 0.89
7 5 0.11
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:40242332 original size:31 final size:31
Alignment explanation
Indices: 40242297--40242360 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
40242287 AAAAAGGAGG
40242297 AAGAAAAATCAAAATCAAAATCAAAAG-CAAA
1 AAGAAAAATCAAAATCAAAATC-AAAGTCAAA
*
40242328 AAGAAAAATCAAAATCAAAGTCAAAGTCAAA
1 AAGAAAAATCAAAATCAAAATCAAAGTCAAA
40242359 AA
1 AA
40242361 ATGAAAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.11
Consensus pattern (31 bp):
AAGAAAAATCAAAATCAAAATCAAAGTCAAA
Found at i:40243478 original size:38 final size:38
Alignment explanation
Indices: 40243427--40243503 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
40243417 GGGCGGCTCA
40243427 AATATTGATCAGATTGGGGCATGTGGTGATCTTGATAT
1 AATATTGATCAGATTGGGGCATGTGGTGATCTTGATAT
40243465 AATATTGATCAGATTGGGGCATGTGGTGATCTTGATAT
1 AATATTGATCAGATTGGGGCATGTGGTGATCTTGATAT
40243503 A
1 A
40243504 CTTGAATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.36
Consensus pattern (38 bp):
AATATTGATCAGATTGGGGCATGTGGTGATCTTGATAT
Found at i:40244462 original size:13 final size:13
Alignment explanation
Indices: 40244444--40244474 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
40244434 GATCATTCTC
40244444 AAAATAAATAAAT
1 AAAATAAATAAAT
40244457 AAAATAAATAAAT
1 AAAATAAATAAAT
40244470 AAAAT
1 AAAAT
40244475 TCTGCAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:40244656 original size:44 final size:42
Alignment explanation
Indices: 40244607--40244833 Score: 121
Period size: 44 Copynumber: 5.2 Consensus size: 42
40244597 GATAACAGAT
*
40244607 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCA-TGACAGTGAAGCAGATCGAAGACAC-AGC
* * * * * * * * *
40244651 CTTGCCTCCCTGGATTACAGTGGAGCAGGTTGAAAATAACAGAT
1 CTTGCCTTCCTGCATGACAGTGAAGCAGATCGAAGA-CACAG-C
* * *
40244695 CTTGTCTTCCTGTATTGACAGTTAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCA-TGACAGTGAAGCAGATCGAAGACA-CAGC
** * * * * ** * * *
40244739 CTTGCCTTCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGCATGACAGTGAAGCAGATCGAAGACA-CAG-C
* * *
40244783 CTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGA
1 CTTGCCTTCCTGCA-TGACAGTGAAGCAGATCGAAGACA-CAGC
40244827 CTTGCCT
1 CTTGCCT
40244834 CCCTAGGTTG
Statistics
Matches: 129, Mismatches: 48, Indels: 12
0.68 0.25 0.06
Matches are distributed among these distances:
43 36 0.28
44 56 0.43
45 37 0.29
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGCATGACAGTGAAGCAGATCGAAGACACAGC
Found at i:40244751 original size:88 final size:87
Alignment explanation
Indices: 40244593--40245578 Score: 1102
Period size: 88 Copynumber: 11.2 Consensus size: 87
40244583 AACAGATCAG
* * *
40244593 TGAAGATAACAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
40244658 CCCTGGATTACAGTGGAGCAGGT
66 TCCTGG-TTGCAGCGGAGCAGGT
* * * * **
40244681 TGAAAATAACAGATCTTGTCTTCCTGTATTGACAGTTAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
40244746 TCCTGGGTTACAGCGGAGCAGGT
66 TCCT-GGTTGCAGCGGAGCAGGT
* * ** *
40244769 TAAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGACTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40244834 CCCTAGGTTGCAGCGGAGTAGGT
66 TCCT-GGTTGCAGCGGAGCAGGT
* * * ** *
40244857 TAAAAATAGCATATCTTGCCTTCCTGCACCGATGGCAAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40244922 CCCTGGATTGCAGTGGAGCAGGT
66 TCCTGG-TTGCAGCGGAGCAGGT
* * ** * *
40244945 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCGGACTTGCC-
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
40245009 TCCTTAGGTTGCAGCGGAGCAGGT
66 TCC-T-GGTTGCAGCGGAGCAGGT
* ** *
40245033 TGAAAAATA-CAGATCTTGCCTTCCTGCACCGATGGCAAAGCAGATCGAAGACACCAGCCTTGCC
1 TG-AAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* *
40245097 TCCCTGGGTTGCAGCAGAGCAGGT
65 TTCCT-GGTTGCAGCGGAGCAGGT
* * ** * * * * * *
40245121 TAAAAATAGCAGATCTTGTCTTCCTGCACCAATAACGAAGCAGACCGAAGACAGCAGACTTTCC-
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
40245185 TCTCTGAGTTGCAGCGGAGCAGGT
66 TC-CTG-GTTGCAGCGGAGCAGGT
* * *
40245209 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCTGATCGAAGACACCAGCCTTGCC-
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40245273 TCTCTAGGTTGCAGCGGAACATGT
66 TC-CT-GGTTGCAGCGGAGCAGGT
* *
40245297 TGAAAATAGCAAATCTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
40245362 TCCTAGGTTGCAGCGGAGCAGGT
66 TCCT-GGTTGCAGCGGAGCAGGT
* * * ** *
40245385 TGAAAATAGCAGATCTTGCCTTCCTTCACCGGCAGCGAAATAGATCGAAGACACTAGCCTTGCC-
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* **
40245449 TCCTTGGATTGTAGTTGAGCAGGT
66 TCC-TGG-TTGCAGCGGAGCAGGT
* * ** * *
40245473 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACCCCAGCCTTACCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
40245538 CCCTGGGTTACAGCGGAGCAAGT
66 TCCT-GGTTGCAGCGGAGCAGGT
40245561 TGAAAAATA-CAGATCTTG
1 TG-AAAATAGCAGATCTTG
40245579 TCTCCCTAAG
Statistics
Matches: 769, Mismatches: 113, Indels: 32
0.84 0.12 0.04
Matches are distributed among these distances:
87 17 0.02
88 729 0.95
89 23 0.03
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (87 bp):
TGAAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
TCCTGGTTGCAGCGGAGCAGGT
Found at i:40245076 original size:264 final size:265
Alignment explanation
Indices: 40244602--40245578 Score: 1304
Period size: 264 Copynumber: 3.7 Consensus size: 265
40244592 GTGAAGATAA
* * *
40244602 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGATT
1 CAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATT
* * * *
40244667 ACAGTGGAGCAGGTTGAAAATAACAGATCTTGTCTTCCTGTATTGACAGTTAAGCAGATCGAAGA
66 GCAGTGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGA
*
40244732 CACCAGCCTTGCCTTCC-TGGGTTACAGCGGAGCAGGTT-AAAAATAGCAGATCTTGCCTTCCTG
131 CACCAGCCTTGCC-TCCTTAGGTTACAGCGGAGCAGGTTGAAAAATAGCAGATCTTGCCTTCCTG
* * * *
40244795 TACTGACAGTTAAGCAGATCGAAGACACCAGACTTGCCTCCCTAGGTTGCAGCGGAGTAGGTTAA
195 CACTGACAGTAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAA
40244860 AAATAG
260 AAATAG
* **
40244866 CATATCTTGCCTTCCTGCACCGATGGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATT
1 CAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATT
*
40244931 GCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGA
66 GCAGTGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGA
* * *
40244996 CACCGGACTTGCCTCCTTAGGTTGCAGCGGAGCAGGTTGAAAAATA-CAGATCTTGCCTTCCTGC
131 CACCAGCCTTGCCTCCTTAGGTTACAGCGGAGCAGGTTGAAAAATAGCAGATCTTGCCTTCCTGC
* ** * * *
40245060 ACCGATGGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAA
196 ACTGACAGTAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAA
40245125 AATAG
261 AATAG
* * * * * * * * * *
40245130 CAGATCTTGTCTTCCTGCACCAATAACGAAGCAGACCGAAGACAGCAGACTTTCCTCTCT-GAGT
1 CAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGA-T
* * * * ** *
40245194 TGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCTGATCGAAG
65 TGCAGTGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAG
* * * *
40245259 ACACCAGCCTTGCCT-CTCTAGGTTGCAGCGGAACATGTTG-AAAATAGCAAATCTTGCCTTCCT
130 ACACCAGCCTTGCCTCCT-TAGGTTACAGCGGAGCAGGTTGAAAAATAGCAGATCTTGCCTTCCT
* * *
40245322 GCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAGGTTGCAGCGGAGCAGGTTG
194 GCACTGACAGTAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTA
40245387 AAAATAG
259 AAAATAG
* * * * *
40245394 CAGATCTTGCCTTCCTTCACCGGCAGCGAAA-TAGATCGAAGACACTAGCCTTGCCTCCTTGGAT
1 CAGATCTTGCCTTCCTGCACCGACAGC-AAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGAT
* * *
40245458 TGTAGTTGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAG
65 TGCAGTGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAG
* * * * *
40245523 ACCCCAGCCTTACCTCCCTGGGTTACAGCGGAGCAAGTTGAAAAATA-CAGATCTTG
130 ACACCAGCCTTGCCTCCTTAGGTTACAGCGGAGCAGGTTGAAAAATAGCAGATCTTG
40245579 TCTCCCTAAG
Statistics
Matches: 613, Mismatches: 91, Indels: 18
0.85 0.13 0.02
Matches are distributed among these distances:
263 13 0.02
264 582 0.95
265 18 0.03
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (265 bp):
CAGATCTTGCCTTCCTGCACCGACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATT
GCAGTGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGA
CACCAGCCTTGCCTCCTTAGGTTACAGCGGAGCAGGTTGAAAAATAGCAGATCTTGCCTTCCTGC
ACTGACAGTAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAA
AATAG
Found at i:40245359 original size:44 final size:43
Alignment explanation
Indices: 40245311--40245542 Score: 110
Period size: 44 Copynumber: 5.3 Consensus size: 43
40245301 AATAGCAAAT
40245311 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTG-CAGTGAAGCAGATCGAAGACACCAGC
** * * * * * * * *
40245355 CTTGCCTTCCTAG-GTTGCAGCGGAGCAGGTTGAAAATAGCAGAT
1 CTTGCCTTCCT-GCACTGCAGTGAAGCAGATCGAAGACACCAG-C
* * * ** *
40245399 CTTGCCTTCCTTCACCGGCAGCGAAATAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCA-CTGCAGTGAAGCAGATCGAAGACACCAGC
* * * * * * * *
40245443 CTTGCC-TCCTTGGATTGTAGTTG-AGCAGGTTGAAGATAGCAGAT
1 CTTGCCTTCC-TGCACTGCAG-TGAAGCAGATCGAAGACACCAG-C
* * *
40245487 CTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACCCCAGC
1 CTTGCCTTCCTGCACTG-CAGTGAAGCAGATCGAAGACACCAGC
* *
40245531 CTTACCTCCCTG
1 CTTGCCTTCCTG
40245543 GGTTACAGCG
Statistics
Matches: 128, Mismatches: 50, Indels: 20
0.65 0.25 0.10
Matches are distributed among these distances:
43 36 0.28
44 55 0.43
45 37 0.29
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (43 bp):
CTTGCCTTCCTGCACTGCAGTGAAGCAGATCGAAGACACCAGC
Found at i:40245716 original size:128 final size:128
Alignment explanation
Indices: 40245559--40246211 Score: 1171
Period size: 128 Copynumber: 5.1 Consensus size: 128
40245549 AGCGGAGCAA
* * **
40245559 GTTGAAAAATACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACGAATCTTAT
1 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
40245624 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
66 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
* *
40245687 GTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAACAGATCGAAGACGGTGAATCTTAT
1 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
40245752 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
66 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
40245815 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
1 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
* * *
40245880 CTTCAAGAGTATGGAAGCAAATTTAAGCCACAAGTCCTATCTCCTTGGTCAGCAGTGGAATAG
66 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
*
40245943 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTAAATCTTAT
1 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
*
40246008 CTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
66 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
* * * *
40246071 GTTAGAAATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTAT
1 GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
40246136 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
66 CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
40246199 GTTGGAAATTACA
1 GTTGGAAATTACA
40246212 AATCCTATCT
Statistics
Matches: 502, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 502 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (128 bp):
GTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAT
CTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAG
Found at i:40247956 original size:24 final size:24
Alignment explanation
Indices: 40247929--40247978 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
40247919 TTACCTTTAA
*
40247929 ATTTCCCTTTAG-ATTTATTTATAT
1 ATTT-CCTTTAGAATTCATTTATAT
* *
40247953 ATTTTCTTTTGAATTCATTTATAT
1 ATTTCCTTTAGAATTCATTTATAT
40247977 AT
1 AT
40247979 ACACATACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.26, C:0.10, G:0.04, T:0.60
Consensus pattern (24 bp):
ATTTCCTTTAGAATTCATTTATAT
Found at i:40260397 original size:7 final size:7
Alignment explanation
Indices: 40260385--40260418 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
40260375 TTAAATGAAT
40260385 TCATTTC
1 TCATTTC
40260392 TCATTTC
1 TCATTTC
40260399 TCATTT-
1 TCATTTC
40260405 TCATTT-
1 TCATTTC
40260411 TCATTTC
1 TCATTTC
40260418 T
1 T
40260419 GAGAAAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (7 bp):
TCATTTC
Found at i:40261913 original size:96 final size:97
Alignment explanation
Indices: 40261748--40261941 Score: 354
Period size: 96 Copynumber: 2.0 Consensus size: 97
40261738 ATGTATGAAA
* *
40261748 CAACACAAATCAACCCCCAACAAATACCTTGATTGTCGTCCAACCCCTTGCATGATTCATGCATG
1 CAACACAAATCAACCCCCAACAAATACCTTGATTATCGTCCAACCCCTTGCATGACTCATGCATG
*
40261813 AAATCAAGCATGAATCAAGCAACCACTTAATC
66 AAATCAAGAATGAATCAAGCAACCACTTAATC
40261845 CAACACAAATCAA-CCCCAACAAATACCTTGATTATCGTCCAACCCCTTGCATGACTCATGCATG
1 CAACACAAATCAACCCCCAACAAATACCTTGATTATCGTCCAACCCCTTGCATGACTCATGCATG
40261909 AAATCAAGAATGAATCAAGCAACCACTTAATC
66 AAATCAAGAATGAATCAAGCAACCACTTAATC
40261941 C
1 C
40261942 TCATCCCACA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 81 0.86
97 13 0.14
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (97 bp):
CAACACAAATCAACCCCCAACAAATACCTTGATTATCGTCCAACCCCTTGCATGACTCATGCATG
AAATCAAGAATGAATCAAGCAACCACTTAATC
Found at i:40264079 original size:17 final size:17
Alignment explanation
Indices: 40264057--40264089 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40264047 TCCCAGATTT
40264057 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
40264074 TGATACCCATATCTTT
1 TGATACCCATATCTTT
40264090 GACTTCCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:40265832 original size:37 final size:37
Alignment explanation
Indices: 40265775--40265880 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
40265765 TATGATCACT
*
40265775 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
40265810 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
40265847 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
40265881 GAAGCTATCA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 55 0.85
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:40265910 original size:46 final size:46
Alignment explanation
Indices: 40265843--40266013 Score: 234
Period size: 46 Copynumber: 3.6 Consensus size: 46
40265833 TAAGTGTAGC
*
40265843 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
40265889 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
40265935 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
40265987 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40266014 AGTACTCAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
46 69 0.62
48 1 0.01
50 1 0.01
52 40 0.36
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:40265965 original size:52 final size:52
Alignment explanation
Indices: 40265886--40265999 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
40265876 TAGCCGAAGC
* **
40265886 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
* *
40265939 TATCACTTTCCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTT-CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
40265991 TATCACTTT
1 TATCACTTT
40266000 GTCACTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 44 0.80
53 11 0.20
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (52 bp):
TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
Found at i:40269802 original size:17 final size:17
Alignment explanation
Indices: 40269776--40269808 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40269766 TCCCAGATTT
*
40269776 TGATATCCATATCTTTC
1 TGATACCCATATCTTTC
40269793 TGATACCCATATCTTT
1 TGATACCCATATCTTT
40269809 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:40276434 original size:6 final size:6
Alignment explanation
Indices: 40276425--40276460 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
40276415 GAATTTGAAC
40276425 TATTTT TATTTT TA-TTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT T
40276461 TAGATTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:40276447 original size:17 final size:17
Alignment explanation
Indices: 40276425--40276459 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40276415 GAATTTGAAC
40276425 TATTTTTATTTTTATTT
1 TATTTTTATTTTTATTT
40276442 TATTTTTATTTTTATTT
1 TATTTTTATTTTTATTT
40276459 T
1 T
40276460 TTAGATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TATTTTTATTTTTATTT
Found at i:40318216 original size:97 final size:96
Alignment explanation
Indices: 40318069--40318279 Score: 273
Period size: 97 Copynumber: 2.2 Consensus size: 96
40318059 AATATTTTTT
* * * ** * *
40318069 AAATTAGATTA-GGTTTCGTGTTTATTGTTTTTAAGAAAAAATCAATTAAATTAGGATTTAGGGT
1 AAATTAGATTAGGGTTTAGAGTTAAAGGTTTTTAAGAAAAAATCAAATAAATTAGGATTCAGGGT
*
40318133 TACTTGAGTAATTTAATTAAAAAAAAATTT-AA
66 TACTTGAGTAAATTAATT--AAAAAAATTTAAA
* *
40318165 AAATTAGATTAGGGTTTAGAGTTAAAGGTTTTTAAGGAAAAATCAAATAAATTAGGGTTCAGGGT
1 AAATTAGATTAGGGTTTAGAGTTAAAGGTTTTTAAGAAAAAATCAAATAAATTAGGATTCAGGGT
* **
40318230 TACTTGAGTAAATTAATTATAAATTTTTAAA
66 TACTTGAGTAAATTAATTAAAAAAATTTAAA
40318261 AAATTAGATTAGGGTTTAG
1 AAATTAGATTAGGGTTTAG
40318280 GGTTTTTAAG
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
95 7 0.07
96 32 0.32
97 61 0.61
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (96 bp):
AAATTAGATTAGGGTTTAGAGTTAAAGGTTTTTAAGAAAAAATCAAATAAATTAGGATTCAGGGT
TACTTGAGTAAATTAATTAAAAAAATTTAAA
Found at i:40318891 original size:18 final size:18
Alignment explanation
Indices: 40318865--40318907 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40318855 GACTAGAAAA
* * *
40318865 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
40318883 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
40318901 AGGATAC
1 AGGATAC
40318908 TCAATTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40319572 original size:7 final size:7
Alignment explanation
Indices: 40319562--40319587 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40319552 CATAATACAT
40319562 AATACTA
1 AATACTA
40319569 AATACTA
1 AATACTA
40319576 AATACTA
1 AATACTA
40319583 AATAC
1 AATAC
40319588 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:40323759 original size:23 final size:23
Alignment explanation
Indices: 40323728--40323774 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
40323718 GGGAAAGATA
*
40323728 AGTTCTTTCTTATCTTTCTCACG
1 AGTTCTTTCTCATCTTTCTCACG
*
40323751 AGTTGTTTCTCATCTTTCTCACG
1 AGTTCTTTCTCATCTTTCTCACG
40323774 A
1 A
40323775 AAGATTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.49
Consensus pattern (23 bp):
AGTTCTTTCTCATCTTTCTCACG
Found at i:40330420 original size:12 final size:12
Alignment explanation
Indices: 40330403--40330427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40330393 CTGGTCTGGA
40330403 AGCTGCTTCAAC
1 AGCTGCTTCAAC
40330415 AGCTGCTTCAAC
1 AGCTGCTTCAAC
40330427 A
1 A
40330428 ATGAGGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
AGCTGCTTCAAC
Found at i:40330591 original size:22 final size:21
Alignment explanation
Indices: 40330528--40330591 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
40330518 TTGCTTCCTT
*
40330528 AACACGCTCCAGGATTTCTTG
1 AACACGCTCCAGGATTTCTTC
* * *
40330549 TACATGCTTCAGGATTTCTTC
1 AACACGCTCCAGGATTTCTTC
*
40330570 AACGCGCTCCAGGATTTTCTTC
1 AACACGCTCCAGGA-TTTCTTC
40330592 TGCAGTTCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (21 bp):
AACACGCTCCAGGATTTCTTC
Found at i:40333456 original size:16 final size:16
Alignment explanation
Indices: 40333431--40333499 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
40333421 TTTGGTTTGC
40333431 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40333447 TGTGTTGGATTAGAGG
1 TGTATTGGATTAGAGG
40333463 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
40333480 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40333496 TGTA
1 TGTA
40333500 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40333477 original size:33 final size:32
Alignment explanation
Indices: 40333431--40333499 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
40333421 TTTGGTTTGC
*
40333431 TGTATTGGATTAGAGGTGTGTTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
40333463 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
40333496 TGTA
1 TGTA
40333500 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:40333564 original size:44 final size:45
Alignment explanation
Indices: 40333480--40333570 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
40333470 GGATTAGAGG
* * *
40333480 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
40333525 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
40333569 TG
1 TG
40333571 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:40333756 original size:18 final size:17
Alignment explanation
Indices: 40333735--40333769 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40333725 TTATTATTAA
*
40333735 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40333753 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40333770 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40333882 original size:14 final size:15
Alignment explanation
Indices: 40333833--40333884 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40333823 TATAAATATA
40333833 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40333848 TATTAAATATATTAT
1 AATTAAATATATTAT
40333863 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40333876 AATTTAATA
1 AATTAAATA
40333885 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40333929 original size:119 final size:121
Alignment explanation
Indices: 40333718--40334006 Score: 494
Period size: 119 Copynumber: 2.4 Consensus size: 121
40333708 ATCATATTTA
40333718 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
40333783 TATTCTTATATGAATTTACTCGAATCATAATATATGATACTAT-AAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
40333837 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
40333902 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
40333958 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAA
40334007 TTTTAAAATA
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
119 105 0.66
120 53 0.33
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:40334022 original size:28 final size:27
Alignment explanation
Indices: 40333958--40334022 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
40333948 AGATAATTTG
*
40333958 AAATAATTA-ATATTAAATATATTTTA
1 AAATAATTATATATTAAATAAATTTTA
*
40333984 ATTAA-AA-TATATGATTTAATAAATTTTA
1 A--AATAATTATAT-ATTAAATAAATTTTA
40334012 AAATAATTATA
1 AAATAATTATA
40334023 ACTAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
26 5 0.16
27 6 0.19
28 20 0.65
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
AAATAATTATATATTAAATAAATTTTA
Found at i:40334056 original size:101 final size:98
Alignment explanation
Indices: 40333950--40334212 Score: 272
Period size: 91 Copynumber: 2.7 Consensus size: 98
40333940 ACTATAAAAG
* *
40333950 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAATTTTAAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAAAATATAT-ATTT-ATAAATTTTAAAA
*
40334015 TAATT-ATAACTAATAAATTATCTTATATGAATTTGT
63 TAATTCATAA-TAATAAATTATCTTATATGAATTTAT
* * * *
40334051 ATAATTTAAAATAATTATTATTACATATAATTTAAT--AATA-ATA--TAT-AATTTCATAA-AA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAATTTTAAAATAA
* * *
40334109 TTCTTGATAATAAATTTTCTTATATGAATTTAT
66 TTCATAATAATAAATTATCTTATATGAATTTAT
* *
40334142 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAA-AATATAT-ATTT-AT-AAATT-TTAA
40334207 TAATAA
61 -AATAA
40334213 AATGTTCTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 25
0.76 0.09 0.14
Matches are distributed among these distances:
91 61 0.46
92 10 0.08
93 2 0.02
94 4 0.03
95 2 0.02
96 2 0.02
97 2 0.02
98 5 0.04
99 2 0.02
100 1 0.01
101 35 0.27
102 2 0.02
103 2 0.02
104 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (98 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAATTTTAAAATAA
TTCATAATAATAAATTATCTTATATGAATTTAT
Found at i:40334079 original size:26 final size:28
Alignment explanation
Indices: 40334050--40334110 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
40334040 TATGAATTTG
*
40334050 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
40334076 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
40334104 TAAAATT
1 TATAATT
40334111 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:40334108 original size:47 final size:46
Alignment explanation
Indices: 40334057--40334200 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
40334047 TTGTATAATT
40334057 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
40334104 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
40334148 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
40334195 TAAAAT
1 TAAAAT
40334201 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:40334120 original size:91 final size:90
Alignment explanation
Indices: 40334025--40334232 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 90
40334015 TAATTATAAC
* * * *
40334025 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
40334090 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
40334116 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
40334181 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
40334207 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
40334233 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 87 0.81
92 21 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:40334192 original size:44 final size:43
Alignment explanation
Indices: 40334050--40334192 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
40334040 TATGAATTTG
* *
40334050 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
40334094 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
40334141 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
40334185 TATAATTT
1 TATAATTT
40334193 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:40334207 original size:47 final size:47
Alignment explanation
Indices: 40334075--40334213 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
40334065 TTATTATTAC
* *
40334075 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
40334122 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
40334166 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
40334213 A
1 A
40334214 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:40336550 original size:104 final size:104
Alignment explanation
Indices: 40336413--40336634 Score: 293
Period size: 104 Copynumber: 2.1 Consensus size: 104
40336403 ATCAGGCACC
* * * * * *
40336413 AACCACTAAGTTAAATACTCGAGTTTATGCGAAAATTACAG-ATCAAAAACAAACTCCTGCTACA
1 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGA-AGAATCAAAAACAAACTCATGCTACA
* * * *
40336477 ATGTAAGAGCTTTGATTCATTATTTACATGAAAATTTTTA
65 ATGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
* * *
40336517 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
1 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGAAGAATCAAAAACAAACTCATGCTACAA
40336582 TGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
66 TGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
* *
40336621 AGCCTCTAAATTTA
1 AACCTCTAAGTTTA
40336635 CAACACATTG
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
103 1 0.01
104 101 0.99
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (104 bp):
AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGAAGAATCAAAAACAAACTCATGCTACAA
TGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
Found at i:40340674 original size:20 final size:20
Alignment explanation
Indices: 40340649--40340687 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40340639 CACGTGGGAT
40340649 GAATGTCT-TCGATGGGACAA
1 GAATGTCTGT-GATGGGACAA
40340669 GAATGTCTGTGATGGGACA
1 GAATGTCTGTGATGGGACA
40340688 GATATTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (20 bp):
GAATGTCTGTGATGGGACAA
Found at i:40342664 original size:22 final size:22
Alignment explanation
Indices: 40342632--40342673 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40342622 TATATAAGCA
* *
40342632 ATATTATTTGAATAGTTATGAG
1 ATATTAGTTGAATAATTATGAG
40342654 ATATTAGTTGAATAATTATG
1 ATATTAGTTGAATAATTATG
40342674 TCACTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (22 bp):
ATATTAGTTGAATAATTATGAG
Found at i:40346222 original size:63 final size:63
Alignment explanation
Indices: 40346100--40346330 Score: 272
Period size: 63 Copynumber: 3.7 Consensus size: 63
40346090 TCTTCGTAGC
* * * * ** * *
40346100 AAACATACATTCAGATAATATATATATATATAATTCATACAATTAAATTCTACTTATAGAACTCA
1 AAACATACATTCGGCTAACATAT-T-TATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
* * *
40346165 AAAAATACATTCGGCTAACATATTTATATAATTTATAAAATTTGTTTCAACTCATAGAACTCA
1 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
* * * *
40346228 AAACATACACT-GGCTAACATATTTATAT--TTCATACAATTAGTTTCAACTTATCA-AACTTA
1 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTAGTTTCAACTCAT-AGAACTCA
40346288 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTA
1 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTA
40346331 AATTCAGCTT
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
60 35 0.25
61 18 0.13
62 17 0.12
63 52 0.37
64 1 0.01
65 19 0.13
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (63 bp):
AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
Found at i:40347949 original size:27 final size:27
Alignment explanation
Indices: 40347918--40347983 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 27
40347908 TGCCCTCCTT
*
40347918 CATCTTCTCCTTCACTTTATTGCCAAC
1 CATCTTCTCCTTCACTTCATTGCCAAC
** * * *
40347945 CATC-TCTGTTTCCCTTCCTTTCCAAC
1 CATCTTCTCCTTCACTTCATTGCCAAC
40347971 CATCTTCTCCTTC
1 CATCTTCTCCTTC
40347984 TGTAACTTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.14, C:0.41, G:0.03, T:0.42
Consensus pattern (27 bp):
CATCTTCTCCTTCACTTCATTGCCAAC
Found at i:40350690 original size:18 final size:17
Alignment explanation
Indices: 40350664--40350699 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40350654 TTTGGTTATA
40350664 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
40350682 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
40350699 T
1 T
40350700 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:40354306 original size:21 final size:21
Alignment explanation
Indices: 40354265--40354307 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40354255 AATAAAGTAG
*
40354265 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
40354286 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
40354307 A
1 A
40354308 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:40354348 original size:33 final size:34
Alignment explanation
Indices: 40354290--40354365 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 34
40354280 TATAGTATTA
*
40354290 TATATTATGATTTTAGTAAATTCATA-TAATAAT
1 TATATTAAGATTTTAGTAAATTCATATTAATAAT
*
40354323 TATATTAAGAATTTTATTAAA-TCATATTTAATAAT
1 TATATTAAG-ATTTTAGTAAATTCATA-TTAATAAT
*
40354358 TATGTTAA
1 TATATTAA
40354366 AATATGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 13 0.35
34 10 0.27
35 14 0.38
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (34 bp):
TATATTAAGATTTTAGTAAATTCATATTAATAAT
Found at i:40354402 original size:24 final size:24
Alignment explanation
Indices: 40354373--40354424 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
40354363 TAAAATATGA
40354373 ATAAATTATTTATTGTTTTTATTC
1 ATAAATTATTTATTGTTTTTATTC
40354397 ATAAATTATTTATTGTTTTTATTC
1 ATAAATTATTTATTGTTTTTATTC
40354421 ATAA
1 ATAA
40354425 TCTTATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
ATAAATTATTTATTGTTTTTATTC
Found at i:40354617 original size:45 final size:43
Alignment explanation
Indices: 40354534--40354619 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
40354524 AACATCATTC
**
40354534 CATTCAACCAAACACAAGAATACTATTACAGTTCTATTCCACT
1 CATTCAACCAAACACAAGAATACTATTACAACTCTATTCCACT
40354577 CATTCAACCAAACA-ATTA-AATTACTTATTACAACTCTATTCCA
1 CATTCAACCAAACACA--AGAA-TAC-TATTACAACTCTATTCCA
40354620 TTACAGTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 1 0.03
43 16 0.43
44 4 0.11
45 16 0.43
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.30
Consensus pattern (43 bp):
CATTCAACCAAACACAAGAATACTATTACAACTCTATTCCACT
Found at i:40374395 original size:40 final size:40
Alignment explanation
Indices: 40374346--40374425 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
40374336 CCTTTCAGGG
40374346 CTCGCGACCTCATCCCTACGAGGCTTACGCAAGCTCCCCT
1 CTCGCGACCTCATCCCTACGAGGCTTACGCAAGCTCCCCT
* * * * * * *
40374386 CTCGTGACCTTATTCTTGCGAGGCTTACGCGAGCTTCCCT
1 CTCGCGACCTCATCCCTACGAGGCTTACGCAAGCTCCCCT
40374426 TACGGGCTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.15, C:0.39, G:0.20, T:0.26
Consensus pattern (40 bp):
CTCGCGACCTCATCCCTACGAGGCTTACGCAAGCTCCCCT
Found at i:40378921 original size:21 final size:21
Alignment explanation
Indices: 40378897--40378936 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40378887 AGCATTCTAC
40378897 CATGAACTTCATCTATTCCCT
1 CATGAACTTCATCTATTCCCT
*
40378918 CATGAACTTCATCTGTTCC
1 CATGAACTTCATCTATTCC
40378937 TGGAGGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.38
Consensus pattern (21 bp):
CATGAACTTCATCTATTCCCT
Found at i:40380489 original size:66 final size:66
Alignment explanation
Indices: 40380378--40380521 Score: 200
Period size: 66 Copynumber: 2.2 Consensus size: 66
40380368 GCAAATCGCT
** * * * *
40380378 CAACTTAAAGCGGATGCAGCATCGAGAGAAGCAGTGGCTAAAAGAAAATATGATGAACTCCAGCT
1 CAACTTAAAATGGAGGCAGCAGCGAGAGAAGCAGAGGCTAAAAGAAAATATGACGAACTCCAGCT
40380443 A
66 A
*
40380444 CAACTTAAAATGGAGGCAGCAGCGAGGGAAGCAGAGGC-AACAAGAAAATATGACGAACTCCAGC
1 CAACTTAAAATGGAGGCAGCAGCGAGAGAAGCAGAGGCTAA-AAGAAAATATGACGAACTCCAGC
40380508 TA
65 TA
40380510 CAACTTCAAAAT
1 CAACTT-AAAAT
40380522 ATGATAGAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 2 0.03
66 62 0.90
67 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (66 bp):
CAACTTAAAATGGAGGCAGCAGCGAGAGAAGCAGAGGCTAAAAGAAAATATGACGAACTCCAGCT
A
Found at i:40380887 original size:44 final size:44
Alignment explanation
Indices: 40380797--40380893 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
40380787 GCGTTTTCCC
* *
40380797 ACAAACGCCGCTATAGAACATGATCTTTAGCTACACTTTTTACT
1 ACAAACGCCGCTAAAGAACATGATCTTTAGCTACACTTTCTACT
* *
40380841 ACAAACGCCGCTAAAGAACATGATCTTTTGC-AGCGC-TTCTAGCT
1 ACAAACGCCGCTAAAGAACATGATCTTTAGCTA-CACTTTCTA-CT
40380885 ACAAACGCC
1 ACAAACGCC
40380894 ACAACATGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 5 0.11
44 42 0.89
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (44 bp):
ACAAACGCCGCTAAAGAACATGATCTTTAGCTACACTTTCTACT
Found at i:40382944 original size:23 final size:23
Alignment explanation
Indices: 40382918--40382964 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40382908 CAAATAATTC
*
40382918 AAAAGTTCAAAAAATTTTAAAAT
1 AAAAGTTCAAAAAATTCTAAAAT
* **
40382941 AAAATTTTTAAAAATTCTAAAAT
1 AAAAGTTCAAAAAATTCTAAAAT
40382964 A
1 A
40382965 TATAAATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAGTTCAAAAAATTCTAAAAT
Found at i:40383046 original size:17 final size:16
Alignment explanation
Indices: 40383018--40383073 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
40383008 GAAAATTTTA
40383018 TTTAAAAATAAAAAAT
1 TTTAAAAATAAAAAAT
40383034 TTTAAAAATTAAAAAA-
1 TTTAAAAA-TAAAAAAT
40383050 -TTAAAAA-AAATACAAT
1 TTTAAAAATAAA-A-AAT
40383066 TTTAAAAA
1 TTTAAAAA
40383074 ACATATTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 9 0.26
16 8 0.23
17 14 0.40
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TTTAAAAATAAAAAAT
Found at i:40383153 original size:19 final size:20
Alignment explanation
Indices: 40383123--40383163 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
40383113 CCAAATATTC
40383123 AAAATTCTAAAAATTCAAAA
1 AAAATTCTAAAAATTCAAAA
40383143 AAAATTC-AAAAATTCAAAA
1 AAAATTCTAAAAATTCAAAA
40383162 AA
1 AA
40383164 GAAGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATTCTAAAAATTCAAAA
Found at i:40385062 original size:30 final size:30
Alignment explanation
Indices: 40385028--40385085 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40385018 AGGTGAGATG
*
40385028 GGGAGGGAATAAAAGTTTTAGGGGAAAAGT
1 GGGAGGGAATAAAAATTTTAGGGGAAAAGT
* *
40385058 GGGAGGGAGTAAAAATTTTGGGGGAAAA
1 GGGAGGGAATAAAAATTTTAGGGGAAAA
40385086 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.41, T:0.19
Consensus pattern (30 bp):
GGGAGGGAATAAAAATTTTAGGGGAAAAGT
Found at i:40385395 original size:9 final size:9
Alignment explanation
Indices: 40385378--40385408 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40385368 TCAAGTTGAT
40385378 TCGAATAAC
1 TCGAATAAC
*
40385387 TCGATTAAC
1 TCGAATAAC
40385396 TCGAATAAC
1 TCGAATAAC
40385405 TCGA
1 TCGA
40385409 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:40387887 original size:11 final size:11
Alignment explanation
Indices: 40387871--40387895 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40387861 TAATAATTAT
40387871 ATTAAAATATG
1 ATTAAAATATG
40387882 ATTAAAATATG
1 ATTAAAATATG
40387893 ATT
1 ATT
40387896 TATTATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTAAAATATG
Found at i:40388009 original size:18 final size:17
Alignment explanation
Indices: 40387968--40388002 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40387958 TAATATGTAT
*
40387968 TAATTCATATTTTAATAA
1 TAATT-ATATTTTAAAAA
40387986 TAATTATATTTTAAAAA
1 TAATTATATTTTAAAAA
40388003 ATGATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTATATTTTAAAAA
Found at i:40396423 original size:15 final size:15
Alignment explanation
Indices: 40396405--40396437 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40396395 TTTTATTTTA
*
40396405 TAAATTATTATAAGG
1 TAAACTATTATAAGG
40396420 TAAACTATTATAAGG
1 TAAACTATTATAAGG
40396435 TAA
1 TAA
40396438 TTTTGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (15 bp):
TAAACTATTATAAGG
Found at i:40426007 original size:26 final size:26
Alignment explanation
Indices: 40425976--40426079 Score: 208
Period size: 26 Copynumber: 4.0 Consensus size: 26
40425966 TTAAACCTTA
40425976 GTTGAAATCGGGCATGAGAACCTTTT
1 GTTGAAATCGGGCATGAGAACCTTTT
40426002 GTTGAAATCGGGCATGAGAACCTTTT
1 GTTGAAATCGGGCATGAGAACCTTTT
40426028 GTTGAAATCGGGCATGAGAACCTTTT
1 GTTGAAATCGGGCATGAGAACCTTTT
40426054 GTTGAAATCGGGCATGAGAACCTTTT
1 GTTGAAATCGGGCATGAGAACCTTTT
40426080 TATTTTTAAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (26 bp):
GTTGAAATCGGGCATGAGAACCTTTT
Found at i:40429185 original size:18 final size:18
Alignment explanation
Indices: 40429162--40429199 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40429152 ACTAAGATAG
40429162 TGGAAAACTCTAGGACAA
1 TGGAAAACTCTAGGACAA
* *
40429180 TGGAAAAGTCTAGGTCAA
1 TGGAAAACTCTAGGACAA
40429198 TG
1 TG
40429200 TAGGGAGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (18 bp):
TGGAAAACTCTAGGACAA
Done.