Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 23 of 27
Found at i:3517335 original size:16 final size:16
Alignment explanation
Indices: 3517266--3517339 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
3517256 GATTCTTAAA
* *
3517266 AAAATGTGAGTTTTAG
1 AAAATCTGATTTTTAG
* *
3517282 AAAATCTAAAATTTTTAA
1 AAAATCT--GATTTTTAG
*
3517300 AAAATCTAAGATTCTT--
1 AAAATCT--GATTTTTAG
3517316 AAAATCTGATTTTTAG
1 AAAATCTGATTTTTAG
3517332 AAAATCTG
1 AAAATCTG
3517340 TGATTGATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.13
16 21 0.45
18 20 0.43
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (16 bp):
AAAATCTGATTTTTAG
Found at i:3518133 original size:18 final size:18
Alignment explanation
Indices: 3518097--3518135 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3518087 GACTTCTTCG
*
3518097 TCAAATATTGACTCCTTA
1 TCAAATATGGACTCCTTA
* *
3518115 TCAAATATGGGCTCTTTA
1 TCAAATATGGACTCCTTA
3518133 TCA
1 TCA
3518136 TCAGGTATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (18 bp):
TCAAATATGGACTCCTTA
Found at i:3519668 original size:16 final size:16
Alignment explanation
Indices: 3519608--3519669 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
3519598 TTGTGGTTAA
* * *
3519608 AAATATATGATTCTAA
1 AAATTTATGATTTTAG
* **
3519624 AAATTTCTGATTACAG
1 AAATTTATGATTTTAG
3519640 AAATTTATGATTTTAG
1 AAATTTATGATTTTAG
3519656 AAATTTATGATTTT
1 AAATTTATGATTTT
3519670 TAAAAAATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (16 bp):
AAATTTATGATTTTAG
Found at i:3519693 original size:19 final size:19
Alignment explanation
Indices: 3519665--3519712 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
3519655 GAAATTTATG
**
3519665 ATTTTT-AAAAAATATGTA
1 ATTTTTAAAAAAATATAAA
*
3519683 ATTTTTAAAAAAATCTAAA
1 ATTTTTAAAAAAATATAAA
3519702 ATTTTTAAAAA
1 ATTTTTAAAAA
3519713 TTCTATGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTTTTAAAAAAATATAAA
Found at i:3519717 original size:18 final size:19
Alignment explanation
Indices: 3519665--3519712 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
3519655 GAAATTTATG
*
3519665 ATTTTTAAAAAATATGT--A
1 ATTTTTAAAAAA-ATCTAAA
3519683 ATTTTTAAAAAAATCTAAA
1 ATTTTTAAAAAAATCTAAA
3519702 ATTTTTAAAAA
1 ATTTTTAAAAA
3519713 TTCTATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.11
18 12 0.44
19 12 0.44
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTTTTAAAAAAATCTAAA
Found at i:3519727 original size:18 final size:17
Alignment explanation
Indices: 3519604--3519729 Score: 64
Period size: 16 Copynumber: 7.4 Consensus size: 17
3519594 ATTATTGTGG
*
3519604 TTAAAAATATATGATTC
1 TTAAAAATTTATGATTC
*
3519621 -TAAAAATTTCTGATTAC
1 TTAAAAATTTATGATT-C
*
3519638 --AGAAATTTATGATT-
1 TTAAAAATTTATGATTC
* *
3519652 TTAGAAATTTATGATTT
1 TTAAAAATTTATGATTC
* *
3519669 TTAAAAA-ATATGTAATTT
1 TTAAAAATTTATG--ATTC
* ** *
3519687 TTAAAAAAATCTAAAATTT
1 TT--AAAAATTTATGATTC
3519706 TTAAAAATTCTATGATTC
1 TTAAAAATT-TATGATTC
3519724 TTAAAA
1 TTAAAA
3519730 TCTGATTTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
16 43 0.50
17 13 0.15
18 17 0.20
19 6 0.07
20 5 0.06
21 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (17 bp):
TTAAAAATTTATGATTC
Found at i:3520185 original size:13 final size:13
Alignment explanation
Indices: 3520151--3520184 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3520141 TTATCTTGTA
3520151 ATGTAAAAATAAT
1 ATGTAAAAATAAT
3520164 ATGTAAAAATAA-
1 ATGTAAAAATAAT
*
3520176 ATTTAAAAA
1 ATGTAAAAA
3520185 AATGATAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
ATGTAAAAATAAT
Found at i:3521653 original size:2 final size:2
Alignment explanation
Indices: 3521646--3521685 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3521636 ACTTCTAGTC
3521646 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
3521686 CTTGTCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3521878 original size:19 final size:19
Alignment explanation
Indices: 3521854--3521891 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3521844 TGAAACAGAC
*
3521854 AGAATGTGTTTTATCCTTG
1 AGAATGTATTTTATCCTTG
3521873 AGAATGTATTTTATCCTTG
1 AGAATGTATTTTATCCTTG
3521892 CTTGAGACTT
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:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
AGAATGTATTTTATCCTTG
Found at i:3525899 original size:68 final size:68
Alignment explanation
Indices: 3525790--3525925 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
3525780 GGAGATAGAG
* * * *
3525790 GTCTATGTGGACAATATGATTGTTAAGTCGTCAAAAGAGAGTGAACATGTCGTCGATCTCTGTAA
1 GTCTATGTGGACAATATGATTGTCAAGTCATCAAAAAAGAGTGAACATGTCATCGATCTCTGTAA
3525855 ACT
66 ACT
*
3525858 GTCTATGTGGACAGTATGATTGTCAAGTCATCAAAAAAGAGTGAACATGTCATCGATCTCTGTAA
1 GTCTATGTGGACAATATGATTGTCAAGTCATCAAAAAAGAGTGAACATGTCATCGATCTCTGTAA
3525923 ACT
66 ACT
3525926 TTTTAAATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (68 bp):
GTCTATGTGGACAATATGATTGTCAAGTCATCAAAAAAGAGTGAACATGTCATCGATCTCTGTAA
ACT
Found at i:3528589 original size:73 final size:72
Alignment explanation
Indices: 3528465--3528666 Score: 273
Period size: 73 Copynumber: 2.8 Consensus size: 72
3528455 AAAGAAACGG
* * * * *
3528465 GGTTAGAATATCCCCTCGAAAATTAC-GGGTTGGAGTATACCCAAGATGAAAATATTTTGGAAAT
1 GGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAA-ATTTTGAAAAT
* *
3528529 AAAACT-G
65 AAAAATAA
3528536 GAGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAACATTTTGAAAA
1 G-GTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAA-ATTTTGAAAA
3528601 TAAAAATAA
64 TAAAAATAA
* * *
3528610 GGTTGGAGTATTCCCTCAAAAATAATGGGGTTGGAGTATCCCCAAGATGAAAAATTT
1 GGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAAATTT
3528667 AATATTTTGA
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
71 1 0.01
72 26 0.22
73 89 0.76
74 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (72 bp):
GGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAAATTTTGAAAATA
AAAATAA
Found at i:3528685 original size:79 final size:72
Alignment explanation
Indices: 3528464--3528701 Score: 271
Period size: 73 Copynumber: 3.2 Consensus size: 72
3528454 AAAAGAAACG
* * * * * *
3528464 GGGTTAGAATATCCCCTCGAAAATTAC-GGGTTGGAGTATACCCAAGATGAAAATATTTTGGAAA
1 GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAATATTTTGAAAA
*
3528528 TAAAACT
66 TAAAAAT
* *
3528535 GGAGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAACATTTTGAAA
1 GG-GTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAATATTTTGAAA
3528600 ATAAAAAT
65 ATAAAAAT
* * *
3528608 AAGGTTGGAGTATTCCCTCAAAAATAATGGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATT
1 -GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATG---AA---AATATT
*
3528673 TTGAAAATAAAAACG
59 TTGAAAATAAAAA-T
3528688 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
3528702 TCGCGATGAA
Statistics
Matches: 142, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
71 2 0.01
72 22 0.15
73 85 0.60
74 1 0.01
76 2 0.01
79 30 0.21
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (72 bp):
GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAAGATGAAAATATTTTGAAAA
TAAAAAT
Found at i:3528701 original size:51 final size:51
Alignment explanation
Indices: 3528636--3528753 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
3528626 CAAAAATAAT
3528636 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGAAAATAAAAAC
1 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGAAAATAAAAAC
* ** * *
3528687 GGGGTTGGAGTATCCTCGCGATGAAAAATTTAATATTTTGGAAATAAAAGC
1 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGAAAATAAAAAC
3528738 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
3528754 TTTGAAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGAAAATAAAAAC
Found at i:3528767 original size:79 final size:78
Alignment explanation
Indices: 3528684--3528950 Score: 263
Period size: 78 Copynumber: 3.4 Consensus size: 78
3528674 TGAAAATAAA
*
3528684 AACGGGGTTGGAGTATCCTCGCGATGAAAAATTTAATA-TTTTGGAAATAAAAGCGGGGTTGGAG
1 AACGGGGTTGGAGTATCC-CGCGATGAAAAATTTAATATTTTTGGAAATAAAAACGGGGTTGGAG
**
3528748 TATCCCTTTGAAAAT
65 TATCCC-TCAAAAAT
* * * * * ***
3528763 AACGGGGTTGGAATATCCCCGTGATGAAAAGTTTGATATTTTTAGAAATAAAAACGAAATTGGAG
1 AACGGGGTTGGAGTAT-CCCGCGATGAAAAATTTAATATTTTTGGAAATAAAAACGGGGTTGGAG
3528828 TATCTCCTCAAAAAT
65 TATC-CCTCAAAAAT
* * ** * *
3528843 AACGGGGTTGGGGTATCCC-CAATGGTAAATTTAATATTTTTGAAAATAAAAATGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCGCGATGAAAAATTTAATATTTTTGGAAATAAAAACGGGGTTGGAGT
**
3528907 ATCCTCTCGGAAAT
66 ATCC-CTCAAAAAT
** *
3528921 AACAAGGTTGGAGTAGCCC-CGA-GAAAAATT
1 AACGGGGTTGGAGTATCCCGCGATGAAAAATT
3528951 CGATGCTTTT
Statistics
Matches: 150, Mismatches: 34, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
77 7 0.05
78 60 0.40
79 34 0.23
80 47 0.31
81 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCGCGATGAAAAATTTAATATTTTTGGAAATAAAAACGGGGTTGGAGT
ATCCCTCAAAAAT
Found at i:3528850 original size:80 final size:79
Alignment explanation
Indices: 3528684--3528894 Score: 221
Period size: 80 Copynumber: 2.7 Consensus size: 79
3528674 TGAAAATAAA
* * * ***
3528684 AACGGGGTTGGAGTATCCTCGCGATGAAAAATTTAATATTTTGGAAATAAAAGCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGCGATGAAAAATTTAATATTTTAGAAATAAAAACGAAATTGGAGT
**
3528749 ATCCCTTTGAAAAT
66 ATCCCTTCAAAAAT
* * * *
3528763 AACGGGGTTGGAATATCCCCGTGATGAAAAGTTTGATATTTTTAGAAATAAAAACGAAATTGGAG
1 AACGGGGTTGGAGTATCCCCGCGATGAAAAATTTAATA-TTTTAGAAATAAAAACGAAATTGGAG
3528828 TATCTCC-TCAAAAAT
65 TATC-CCTTCAAAAAT
* * ** *
3528843 AACGGGGTTGGGGTAT-CCC-CAATGGTAAATTTAATATTTTTGAAAATAAAAA
1 AACGGGGTTGGAGTATCCCCGCGATGAAAAATTTAATATTTTAG-AAATAAAAA
3528895 TGGGGTTGGA
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
77 5 0.05
78 20 0.19
79 36 0.33
80 45 0.42
81 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGCGATGAAAAATTTAATATTTTAGAAATAAAAACGAAATTGGAGT
ATCCCTTCAAAAAT
Found at i:3531381 original size:20 final size:20
Alignment explanation
Indices: 3531356--3531395 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3531346 TTTTAAGCAT
*
3531356 GTATCGATACATTTTCTTAA
1 GTATCGATACATTTCCTTAA
3531376 GTATCGATACATTTCCTTAA
1 GTATCGATACATTTCCTTAA
3531396 TAGTACGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTCCTTAA
Found at i:3531486 original size:21 final size:20
Alignment explanation
Indices: 3531436--3531487 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
3531426 TTTTAGGCAA
3531436 GTATTGATACATTCACTCAT
1 GTATTGATACATTCACTCAT
** *
3531456 GTATCAATACATTTACT-ATTT
1 GTATTGATACATTCACTCA--T
3531477 GTATTGATACA
1 GTATTGATACA
3531488 AATTGTAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.56
21 10 0.40
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (20 bp):
GTATTGATACATTCACTCAT
Found at i:3532782 original size:21 final size:20
Alignment explanation
Indices: 3532758--3532822 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
3532748 TTTTAAAAAA
3532758 AAAGCAAACGAAAAAAAAAGC
1 AAAGCAAA-GAAAAAAAAAGC
* *
3532779 AAAGCAAAGCAAAAATAAG-
1 AAAGCAAAGAAAAAAAAAGC
*
3532798 AAAGCAAAAAAGATAAAAAAGC
1 AAAGCAAAGAA-A-AAAAAAGC
3532820 AAA
1 AAA
3532823 AAATAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.25
20 10 0.28
21 14 0.39
22 3 0.08
ACGTcount: A:0.72, C:0.11, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAGCAAAGAAAAAAAAAGC
Found at i:3532818 original size:17 final size:17
Alignment explanation
Indices: 3532755--3532836 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 17
3532745 TTTTTTTAAA
*
3532755 AAAAAAGCAAACGAAAAAA
1 AAAAAAGCAAA--AAAAAT
3532774 AAAGCAAAGCAAAGCAAAAAT
1 AAA--AAAGCAAA--AAAAAT
* *
3532795 AAGAAAGCAAAAAAGAT
1 AAAAAAGCAAAAAAAAT
3532812 AAAAAAGCAAAAAATAAT
1 AAAAAAGCAAAAAA-AAT
3532830 AATAAAA
1 AA-AAAA
3532837 CTCAGATGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 18 0.35
18 4 0.08
19 15 0.29
21 15 0.29
ACGTcount: A:0.74, C:0.09, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAAGCAAAAAAAAT
Found at i:3534263 original size:28 final size:28
Alignment explanation
Indices: 3534165--3534354 Score: 133
Period size: 28 Copynumber: 7.0 Consensus size: 28
3534155 GATAGCACTT
**
3534165 AAGTCAAAGCCCACATTTGTTGGCATC-C
1 AAGTCAAAGCCCACATTCATTGGCA-CAC
***
3534193 AAGTCAAA-CCCACATTTGCTGG--CAC
1 AAGTCAAAGCCCACATTCATTGGCACAC
3534218 AAGTCAAAGCCCACATTCATTGGCACAC
1 AAGTCAAAGCCCACATTCATTGGCACAC
* * ***
3534246 AAGTCTAAGCCCACATTCACTGGCATGT
1 AAGTCAAAGCCCACATTCATTGGCACAC
** * * *
3534274 AAGTCGGAGCCCATACTT-ATTAG--CAT
1 AAGTCAAAGCCCACA-TTCATTGGCACAC
* *
3534300 AAGTCAAAGCCCACATTCGTTGTCACAC
1 AAGTCAAAGCCCACATTCATTGGCACAC
* * *
3534328 AAGTCTAAGCCTACATTCACTGGCACA
1 AAGTCAAAGCCCACATTCATTGGCACA
3534355 TAAATCAATA
Statistics
Matches: 126, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
24 1 0.01
25 11 0.09
26 26 0.21
27 13 0.10
28 73 0.58
29 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (28 bp):
AAGTCAAAGCCCACATTCATTGGCACAC
Found at i:3534406 original size:28 final size:27
Alignment explanation
Indices: 3534365--3534464 Score: 92
Period size: 28 Copynumber: 3.6 Consensus size: 27
3534355 TAAATCAATA
*
3534365 CCACACTAGCTGGCACTTGAGTCAAAGC
1 CCACACTAGTTGGCACTT-AGTCAAAGC
* * *
3534393 CCACACTAGTTGGCACCTACATCGAAGC
1 CCACACTAGTTGGCACTTA-GTCAAAGC
* * * *
3534421 CCACATTAGTTAGCATCTAAGTCAAAGT
1 CCACACTAGTTGGCA-CTTAGTCAAAGC
*
3534449 CCACACCAGTTGGCAC
1 CCACACTAGTTGGCAC
3534465 CTCGTAGGGA
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
27 2 0.04
28 52 0.93
29 2 0.04
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (27 bp):
CCACACTAGTTGGCACTTAGTCAAAGC
Found at i:3540375 original size:22 final size:23
Alignment explanation
Indices: 3540350--3540393 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3540340 TACACGACAA
*
3540350 AAAAAATAATA-TAATATAATAT
1 AAAAAATAATACAAATATAATAT
3540372 AAAAAATAATACAAATATAATA
1 AAAAAATAATACAAATATAATA
3540394 AGAATATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAAATAATACAAATATAATAT
Found at i:3543798 original size:27 final size:27
Alignment explanation
Indices: 3543760--3543812 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3543750 AAACATTTTT
3543760 AATATAATTTTAATAATATTAAATATA
1 AATATAATTTTAATAATATTAAATATA
* *
3543787 AATATAATTTTAATAATTTTTAATAT
1 AATATAATTTTAATAATATTAAATAT
3543813 TTTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATAATTTTAATAATATTAAATATA
Found at i:3543811 original size:21 final size:21
Alignment explanation
Indices: 3543754--3543820 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 21
3543744 AAGTCAAAAC
3543754 ATTTTTAATATAATTTTAATA
1 ATTTTTAATATAATTTTAATA
3543775 ATATTAAATATAAATATAATTTTAATA
1 AT-TT---T-T-AATATAATTTTAATA
3543802 ATTTTTAATAT--TTTTAATA
1 ATTTTTAATATAATTTTAATA
3543821 TTAATTTAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
19 8 0.20
21 7 0.17
22 3 0.08
23 1 0.03
25 1 0.03
26 3 0.08
27 17 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTAATATAATTTTAATA
Found at i:3543821 original size:9 final size:9
Alignment explanation
Indices: 3543794--3543842 Score: 53
Period size: 9 Copynumber: 5.0 Consensus size: 9
3543784 ATAAATATAA
3543794 TTTTAATAAT
1 TTTTAAT-AT
3543804 TTTTAATAT
1 TTTTAATAT
3543813 TTTTAATAT
1 TTTTAATAT
*
3543822 TAATTTAACAAT
1 T--TTTAA-TAT
3543834 TTTTAATAT
1 TTTTAATAT
3543843 AATTTTAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 14 0.41
10 12 0.35
11 5 0.15
12 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAATAT
Found at i:3543849 original size:21 final size:20
Alignment explanation
Indices: 3543754--3543849 Score: 76
Period size: 21 Copynumber: 4.9 Consensus size: 20
3543744 AAGTCAAAAC
3543754 ATTTTTAATATAATTTTAATA
1 ATTTTTAATATAATTTTAA-A
* * * *
3543775 ATATTAAATATAA--ATATA
1 ATTTTTAATATAATTTTAAA
* *
3543793 A-TTTTAATA-ATTTTTAAT
1 ATTTTTAATATAATTTTAAA
3543811 ATTTTTAATATTAA-TTTAACA
1 ATTTTTAATA-TAATTTTAA-A
3543832 ATTTTTAATATAATTTTA
1 ATTTTTAATATAATTTTA
3543850 GTACCACGAT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
16 1 0.02
17 6 0.11
18 5 0.09
19 10 0.18
20 8 0.14
21 26 0.46
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTAATATAATTTTAAA
Found at i:3549131 original size:72 final size:72
Alignment explanation
Indices: 3548944--3549263 Score: 466
Period size: 72 Copynumber: 4.5 Consensus size: 72
3548934 TGATAATTCA
* * * *
3548944 AGATAATCTACATGATAAATACAATCAACAACTATTTTTGCATATTTAAAACTACTATC-AC--C
1 AGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAAC
3549006 TTAAATCCG
66 -T-AATCCG
* * * *
3549015 AGATAATCTGCACGATAAATATAATCAACAACTATTTTTGCATATTTAAAACTACTATCAACAAT
1 AGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAAC
*
3549080 TAATTCG
66 TAATCCG
* *
3549087 AGATAATCTGCACAATAACTACAATCAACAACTATTTCTCCATATTTAAAACTACTATCAACAAC
1 AGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAAC
3549152 TAATCCG
66 TAATCCG
* * *
3549159 AGATAATCTGCATGATAACTACAATCAACAAATATTTCTGCATATTTAAAATTACTATCAACAAC
1 AGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAAC
3549224 TAATCCG
66 TAATCCG
*
3549231 AGATAATCTGCACAATAACTACAATCAACAACT
1 AGATAATCTGCACGATAACTACAATCAACAACT
3549264 TTGTGTGCCA
Statistics
Matches: 226, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
71 56 0.25
72 169 0.75
73 1 0.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (72 bp):
AGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAAC
TAATCCG
Found at i:3549140 original size:33 final size:33
Alignment explanation
Indices: 3549037--3549225 Score: 99
Period size: 33 Copynumber: 5.4 Consensus size: 33
3549027 CGATAAATAT
* *
3549037 AATCAACAACTATTTTTGCATATTTAAAACTAC
1 AATCAACAACTATTTCTACATATTTAAAACTAC
* * * * * *
3549070 TATCAACAATTAATTCGAGATAATCTGCACAATAACTAC
1 AATCAACAACTATTTCTACAT-AT-T---TAA-AACTAC
*
3549109 AATCAACAACTATTTCTCCATATTTAAAACTAC
1 AATCAACAACTATTTCTACATATTTAAAACTAC
* * * * * *
3549142 TATCAACAACTAATCCGAGATAATCTGCATGATAACTAC
1 AATCAACAACTATTTCTACAT-AT-T---T-AAAACTAC
* * *
3549181 AATCAACAAATATTTCTGCATATTTAAAATTAC
1 AATCAACAACTATTTCTACATATTTAAAACTAC
*
3549214 TATCAACAACTA
1 AATCAACAACTA
3549226 ATCCGAGATA
Statistics
Matches: 111, Mismatches: 33, Indels: 24
0.66 0.20 0.14
Matches are distributed among these distances:
33 51 0.46
34 7 0.06
35 2 0.02
37 2 0.02
38 7 0.06
39 42 0.38
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (33 bp):
AATCAACAACTATTTCTACATATTTAAAACTAC
Found at i:3549553 original size:27 final size:27
Alignment explanation
Indices: 3549523--3549581 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
3549513 TAGGTCGTGA
*
3549523 TAGGATATGATGGGTAT-AGAGGTTGAG
1 TAGGATATGACGGGTATGA-AGGTTGAG
3549550 TAGGATATGACGGGTATGAAGGTTGAG
1 TAGGATATGACGGGTATGAAGGTTGAG
3549577 TAGGA
1 TAGGA
3549582 AGATATGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.27
Consensus pattern (27 bp):
TAGGATATGACGGGTATGAAGGTTGAG
Found at i:3554644 original size:32 final size:31
Alignment explanation
Indices: 3554582--3554648 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
3554572 ACCCCTAAAC
* *
3554582 TAATTACTTTAAACCTAATTCAACATAATAA
1 TAATTACTATAAACCTAATTCAACAAAATAA
3554613 GTAATTACTATAAA-CTAATT-ACACAAAAATAA
1 -TAATTACTATAAACCTAATTCA-AC-AAAATAA
3554645 TAAT
1 TAAT
3554649 AAAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 1 0.03
31 12 0.39
32 18 0.58
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.33
Consensus pattern (31 bp):
TAATTACTATAAACCTAATTCAACAAAATAA
Found at i:3554787 original size:21 final size:21
Alignment explanation
Indices: 3554747--3554796 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3554737 AAATTTTAAC
* *
3554747 ATATTAAAAAAATAATAATAA
1 ATATTAAAAAAAGAAAAATAA
3554768 A-ATTAAAAAACAGAAAAATAA
1 ATATTAAAAAA-AGAAAAATAA
3554789 ATATTAAA
1 ATATTAAA
3554797 TTACCTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 10 0.40
22 6 0.24
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
ATATTAAAAAAAGAAAAATAA
Found at i:3556815 original size:2 final size:2
Alignment explanation
Indices: 3556808--3556841 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3556798 ACTTCTAGTC
3556808 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
3556842 CTTGTCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3557205 original size:25 final size:24
Alignment explanation
Indices: 3557154--3557212 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
3557144 AGTCAATTTT
* ** *
3557154 TTTTTTAAAATTTTGATTTTTTTA
1 TTTTTTAAAATTTTAATTAATTAA
3557178 TTTTTTAAATATTTTAATTAATTAA
1 TTTTTTAAA-ATTTTAATTAATTAA
*
3557203 TTTTATAAAA
1 TTTTTTAAAA
3557213 CATATATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTTTAAAATTTTAATTAATTAA
Found at i:3564077 original size:27 final size:26
Alignment explanation
Indices: 3564031--3564210 Score: 130
Period size: 28 Copynumber: 6.7 Consensus size: 26
3564021 GATAGTACCT
3564031 AAGTCAAAGCCCACATTTGTTGCCATCC
1 AAGTCAAAGCCCACATTTGTTGCCA--C
* * *
3564059 GAGTCAAA-CCCACACTTGTTGGCAC
1 AAGTCAAAGCCCACATTTGTTGCCAC
3564084 AAGTCAAAGCCCACATTTGTTAGCACAC
1 AAGTCAAAGCCCACATTTGTT-GC-CAC
* *** *
3564112 AACTCTAAA-CCCACATTCACTGGCAC
1 AAGTC-AAAGCCCACATTTGTTGCCAC
* * *
3564138 GTAAGTCGAAGCCCATATTTGTTGGCAC
1 --AAGTCAAAGCCCACATTTGTTGCCAC
* *
3564166 AAGTCAAAGCCCATATTCGTTGGCACAC
1 AAGTCAAAGCCCACATTTGTT-GC-CAC
* *
3564194 AAGTCTAAGCCTACATT
1 AAGTCAAAGCCCACATT
3564211 CATTGGCACA
Statistics
Matches: 120, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
25 8 0.07
26 33 0.28
27 19 0.16
28 57 0.47
29 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (26 bp):
AAGTCAAAGCCCACATTTGTTGCCAC
Found at i:3564198 original size:54 final size:53
Alignment explanation
Indices: 3564031--3564210 Score: 159
Period size: 54 Copynumber: 3.3 Consensus size: 53
3564021 GATAGTACCT
* *
3564031 AAGTCAAAGCCCACATTTGTTGCCATCCGAGTCAAACCCACACTT-GTTGG--CAC
1 AAGTCAAAGCCCACATTTGTTGACA--CAAGTCAAACCCACA-TTCGTTGGCACAC
* ** **
3564084 AAGTCAAAGCCCACATTTGTTAGCACACAACTCTAAACCCACATTCACTGGCACGT
1 AAGTCAAAGCCCACATTTGTT-G-ACACAAGTC-AAACCCACATTCGTTGGCACAC
* * * *
3564140 AAGTCGAAGCCCATATTTGTTGGCACAAGTCAAAGCCCATATTCGTTGGCACAC
1 AAGTCAAAGCCCACATTTGTTGACACAAGTCAAA-CCCACATTCGTTGGCACAC
* *
3564194 AAGTCTAAGCCTACATT
1 AAGTCAAAGCCCACATT
3564211 CATTGGCACA
Statistics
Matches: 101, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
53 30 0.30
54 48 0.48
55 3 0.03
56 20 0.20
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (53 bp):
AAGTCAAAGCCCACATTTGTTGACACAAGTCAAACCCACATTCGTTGGCACAC
Found at i:3564245 original size:28 final size:28
Alignment explanation
Indices: 3564214--3564292 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
3564204 CTACATTCAT
* *
3564214 TGGCACATAAATCAATA-CCCACACTAGC
1 TGGCACCTAAATCAA-AGCCCACACTAGA
* *
3564242 TGGCACCTGAGTCAAAGCCCACACTAGA
1 TGGCACCTAAATCAAAGCCCACACTAGA
*
3564270 TGGCACCTACATCAAAGCCCACA
1 TGGCACCTAAATCAAAGCCCACA
3564293 TGAGTTAGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.35, C:0.34, G:0.15, T:0.15
Consensus pattern (28 bp):
TGGCACCTAAATCAAAGCCCACACTAGA
Found at i:3564246 original size:82 final size:81
Alignment explanation
Indices: 3564062--3564264 Score: 235
Period size: 82 Copynumber: 2.5 Consensus size: 81
3564052 GCCATCCGAG
*
3564062 TCAAACCCACACTTGTTGGCACAAGTCAAAGCCCACATTTGTTAGCACACAACTCTAAACCCACA
1 TCAAACCCACACTTGTTGGCACAAGTCAAAGCCCACATTCGTTAGCACACAACTCTAAACCCACA
* *
3564127 TTCACTGGCACGTAAG
66 TTCACTGGCACATAAA
* * * * * * * *
3564143 TCGAAGCCCATATTTGTTGGCACAAGTCAAAGCCCATATTCGTTGGCACACAAGTCTAAGCCTAC
1 TC-AAACCCACACTTGTTGGCACAAGTCAAAGCCCACATTCGTTAGCACACAACTCTAAACCCAC
*
3564208 ATTCATTGGCACATAAA
65 ATTCACTGGCACATAAA
* * *
3564225 TCAATACCCACACTAGCTGGCACCTGAGTCAAAGCCCACA
1 TCAA-ACCCACACTTGTTGGCA-C-AAGTCAAAGCCCACA
3564265 CTAGATGGCA
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
81 4 0.04
82 81 0.82
83 1 0.01
84 13 0.13
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.22
Consensus pattern (81 bp):
TCAAACCCACACTTGTTGGCACAAGTCAAAGCCCACATTCGTTAGCACACAACTCTAAACCCACA
TTCACTGGCACATAAA
Found at i:3564312 original size:28 final size:29
Alignment explanation
Indices: 3564231--3564314 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 29
3564221 TAAATCAATA
* * *
3564231 CCCACACTAGCTGGCACCT-GAGTCAAAG
1 CCCACACTAGATAGCACCTACAGTCAAAG
*
3564259 CCCACACTAGATGGCACCTACA-TCAAAG
1 CCCACACTAGATAGCACCTACAGTCAAAG
* *
3564287 CCCACA-TGAGTTAGCATCTA-AGTCAAAG
1 CCCACACT-AGATAGCACCTACAGTCAAAG
3564315 TCCAGAACAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 2 0.04
28 45 0.94
29 1 0.02
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.17
Consensus pattern (29 bp):
CCCACACTAGATAGCACCTACAGTCAAAG
Found at i:3564645 original size:4 final size:4
Alignment explanation
Indices: 3564638--3564664 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3564628 GAAAAAATAC
3564638 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3564665 AAGAATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3580176 original size:63 final size:63
Alignment explanation
Indices: 3580089--3580246 Score: 210
Period size: 63 Copynumber: 2.5 Consensus size: 63
3580079 CACTTTTCTC
* * * * *
3580089 TTTCTTTTAAAAGCCCACATAAGTTGGTGGCACATGTTTAGTCCTCAAAAAAGTAGGAAGTC-TT
1 TTTCTTTT-AAAGCCCACACAAGTTGGTGACACATGTTTAGTCCTC-AAAAAGCAAGAAGCCTTT
* *
3580153 TTTCTTTTAAAGCCCACACAAGTTGGTGACACATGTTTAGTCCTCAAAGAGCAAGACGCCTTT
1 TTTCTTTTAAAGCCCACACAAGTTGGTGACACATGTTTAGTCCTCAAAAAGCAAGAAGCCTTT
* *
3580216 TTTTTTTTAAAGCCCACACAAGTTGGCGACA
1 TTTCTTTTAAAGCCCACACAAGTTGGTGACA
3580247 GACCCTTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
62 10 0.12
63 66 0.79
64 8 0.10
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (63 bp):
TTTCTTTTAAAGCCCACACAAGTTGGTGACACATGTTTAGTCCTCAAAAAGCAAGAAGCCTTT
Found at i:3580354 original size:62 final size:61
Alignment explanation
Indices: 3580261--3580666 Score: 187
Period size: 62 Copynumber: 6.7 Consensus size: 61
3580251 CTTTTTTTTT
** * *
3580261 AAAGCCCACACAAGTTGGTGGCACCCGTTTAGACTTCAAAAAGCAGGACACTTTTTTTAAAA
1 AAAGCCCACACAAGTTGGTAACACCCATTTAGACCTCAAAAAGCAGGAC-CTTTTTTTAAAA
* * * * ***
3580323 AAAGCCTACACAAGTTGGTAACACCTATTTAGTCCTCAAAGAGCAGGACCTTTTTTCT-TTT
1 AAAGCCCACACAAGTTGGTAACACCCATTTAGACCTCAAAAAGCAGGACCTTTTTT-TAAAA
* * * ** * * * * *
3580384 AAAGCCGACACAAATAGGTGGCACCCATTTAGTCCTCAAAGAGCATGA-C--ATTTTCAAA
1 AAAGCCCACACAAGTTGGTAACACCCATTTAGACCTCAAAAAGCAGGACCTTTTTTTAAAA
* * ** * ** *
3580442 AAA-CCCATAAAAGTTGGTGGCA-CCAGTTTAGTCCTCAAAAAATAGAACATCTTTTTTT--AA
1 AAAGCCCACACAAGTTGGTAACACCCA-TTTAGACCTCAAAAAGCAGGAC--CTTTTTTTAAAA
** * * *
3580502 AAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGATGCC-TTTTTT----
1 AAAGCCCACACAAGTTGGTAACACCCATTTAGACCTCAAAAAGCAGGA--CCTTTTTTTAAAA
* ** * * **
3580560 AAAGCCCGCACAAGTTGGTGGCACCCGTTTA-ATCCTCAAAAAGTAGGACGCCTTTTTCTT--TT
1 AAAGCCCACACAAGTTGGTAACACCCATTTAGA-CCTCAAAAAGCAGGA--CCTTTTT-TTAAAA
** * * *
3580622 AAAGCCCACACAAGTTGGTGGCACCCGTTTGGTCCTCAAAAAGCA
1 AAAGCCCACACAAGTTGGTAACACCCATTTAGACCTCAAAAAGCA
3580667 AGATGCCTCT
Statistics
Matches: 277, Mismatches: 49, Indels: 36
0.77 0.14 0.10
Matches are distributed among these distances:
56 3 0.01
57 31 0.11
58 52 0.19
59 4 0.01
60 15 0.05
61 83 0.30
62 88 0.32
63 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (61 bp):
AAAGCCCACACAAGTTGGTAACACCCATTTAGACCTCAAAAAGCAGGACCTTTTTTTAAAA
Found at i:3580414 original size:61 final size:60
Alignment explanation
Indices: 3580247--3580666 Score: 382
Period size: 61 Copynumber: 7.0 Consensus size: 60
3580237 GTTGGCGACA
* * *
3580247 GACCCTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGACTTCAAAAAGCAG
1 GACCTTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
*** * ** ** *
3580307 GACACTTTTTTTAAAAAAAGCCTACACAAGTTGGTAACACCTATTTAGTCCTCAAAGAGCAG
1 GAC-CTTTTTTT-TTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
* * * * * *
3580369 GACCTTTTTTCTTTTAAAGCCGACACAAATAGGTGGCACCCATTTAGTCCTCAAAGAGCAT
1 GACCTTTTTT-TTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
* *** * * * * **
3580430 GA-C--ATTTTCAAAAAACCCATAAAAGTTGGTGGCACCAGTTTAGTCCTCAAAAAATAG
1 GACCTTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
* * ** *
3580487 AACATCTTTTTTTAAAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAG
1 GACCT-TTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
*** * * *
3580548 GA--TGCCTTTTTTAAAGCCCGCACAAGTTGGTGGCACCCGTTTAATCCTCAAAAAGTAG
1 GACCTTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
* *
3580606 GACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTGGTCCTCAAAAAGCA
1 GA--CCTTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCA
3580667 AGATGCCTCT
Statistics
Matches: 282, Mismatches: 67, Indels: 20
0.76 0.18 0.05
Matches are distributed among these distances:
57 36 0.13
58 51 0.18
59 1 0.00
60 4 0.01
61 101 0.36
62 89 0.32
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (60 bp):
GACCTTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAG
Found at i:3580688 original size:179 final size:178
Alignment explanation
Indices: 3580250--3580703 Score: 451
Period size: 179 Copynumber: 2.5 Consensus size: 178
3580240 GGCGACAGAC
* * *
3580250 CCTTTTT-TTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGACTTCAAAAAGCAGGACACTT
1 CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAAGACACTT
* ** * ***
3580314 TTTTTAAAAAAAGCCTACACAAGTTGGTAACACCTATTTAGTCCTCAAAGAGCAGGACCTTTTTT
66 TTTTT---AAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGA-CTGCCTT
* *
3580379 CTTTTAAAGCCGACACAAATAGGTGGCACCCATTTAGTCCTCAAAGAGCATG
127 CTTTTAAAGCCGACACAAATAGGTGGCACCCATTTAATCCTCAAAGAGCACG
* * ** * * * *
3580431 ACATTTTC--AAAAAACCCATAAAAGTTGGTGGCACCAGTTTAGTCCTCAAAAA--ATAGAACAT
1 CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCA-AG-ACA-
*
3580492 CTTTTTTTAAAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGA-TGCCTT
63 CTTTTTTT-AAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGACTGCCTT
* * * *
3580556 -TTTTAAAGCCCG-CACAAGTTGGTGGCACCCGTTTAATCCTCAAAAAGTAGGACG
127 CTTTTAAAG-CCGACACAAATAGGTGGCACCCATTTAATCCTC--AAAG-AGCACG
*
3580610 CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTGGTCCTCAAAAAGCAAGATGC-C
1 CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAAGA--CAC
* * *
3580674 TCTTTTT-AAAGCCCACCCAAGTCGGTGGCA
64 TTTTTTTAAAAGCCCACACAAGTTGGTGGCA
3580704 ACCTTTTCTA
Statistics
Matches: 222, Mismatches: 37, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
176 33 0.15
177 6 0.03
178 5 0.02
179 77 0.35
180 39 0.18
181 58 0.26
182 2 0.01
183 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (178 bp):
CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAAAGCAAGACACTT
TTTTTAAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGACTGCCTTCTTT
TAAAGCCGACACAAATAGGTGGCACCCATTTAATCCTCAAAGAGCACG
Found at i:3580716 original size:32 final size:32
Alignment explanation
Indices: 3580675--3580793 Score: 125
Period size: 32 Copynumber: 3.7 Consensus size: 32
3580665 CAAGATGCCT
* *
3580675 CTTTT-TAAAGCCCACCCAAGTCGGTGGCAAC
1 CTTTTCTAAAGCCCACACAAGTCAGTGGCAAC
*
3580706 CTTTTCTAAAGTCCACACAAGTCAGTGGCAACC
1 CTTTTCTAAAGCCCACACAAGTCAGTGGCAA-C
** * *
3580739 CCCTTC-AAAGCCCGCACAAGTTAGTGGCAAC
1 CTTTTCTAAAGCCCACACAAGTCAGTGGCAAC
* *
3580770 TCTATTCTAAAGTCCACACAAGTC
1 -CTTTTCTAAAGCCCACACAAGTC
3580794 GATGGCATTT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.08
32 47 0.66
33 18 0.25
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (32 bp):
CTTTTCTAAAGCCCACACAAGTCAGTGGCAAC
Found at i:3580915 original size:51 final size:51
Alignment explanation
Indices: 3580809--3581015 Score: 218
Period size: 52 Copynumber: 4.0 Consensus size: 51
3580799 CATTTCCTTC
* * *
3580809 TAAGCCCAATGTCGCTGACCTTGAATTAGTACACTGGCACCCTTTTCATTTT
1 TAAGCCCAATGTCGCTGGCCTTGAATTAGCACACTGGCACCCTTGTCA-TTT
* * *
3580861 TAAGCCCAATGTCGTTGGCCTTGAA-TAGCACACTAGCACCCTTGTCGTGTT
1 TAAGCCCAATGTCGCTGGCCTTGAATTAGCACACTGGCACCCTTGTCAT-TT
* * * * * *
3580912 TAAGCCCAATGTTGCTAGTCTTGAACTAGCCCACTGGCACCATTGTCATTT
1 TAAGCCCAATGTCGCTGGCCTTGAATTAGCACACTGGCACCCTTGTCATTT
* * * * * *
3580963 CTAAGCCCGATCTCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCATTT
1 -TAAGCCCAATGTCGCTGGCCTTGAATTAGCACACTGGCACCCTTGTCATTT
3581015 T
1 T
3581016 TAAACCTTGA
Statistics
Matches: 127, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
50 1 0.01
51 44 0.35
52 82 0.65
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (51 bp):
TAAGCCCAATGTCGCTGGCCTTGAATTAGCACACTGGCACCCTTGTCATTT
Found at i:3582477 original size:13 final size:13
Alignment explanation
Indices: 3582438--3582478 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3582428 CTCTTTGTGA
*
3582438 TATTTTTTCATTT
1 TATTTTTTTATTT
*
3582451 AATTTTTTTA--T
1 TATTTTTTTATTT
3582462 TATTTTTTTATTT
1 TATTTTTTTATTT
3582475 TATT
1 TATT
3582479 ATTATTGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 10 0.43
13 13 0.57
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:3589151 original size:3 final size:3
Alignment explanation
Indices: 3589130--3589168 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
3589120 ATTAACAAAC
3589130 AAT AAT AAAT AA- AACT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT -AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
3589169 CGGGGACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 26 0.79
4 5 0.15
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3589389 original size:27 final size:27
Alignment explanation
Indices: 3589355--3589407 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3589345 TACAACATGA
* *
3589355 AAAAATAATTA-AAATATAATATGAATC
1 AAAAATAA-TACAAATACAATAAGAATC
3589382 AAAAATAATACAAATACAATAAGAAT
1 AAAAATAATACAAATACAATAAGAAT
3589408 ATATCAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAATAATACAAATACAATAAGAATC
Found at i:3589608 original size:20 final size:20
Alignment explanation
Indices: 3589583--3589621 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3589573 TGTTTAAAAT
3589583 TTTCATAAAATAACGAGAAA
1 TTTCATAAAATAACGAGAAA
3589603 TTTCATAAAATAACGAGAA
1 TTTCATAAAATAACGAGAA
3589622 TTCATGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (20 bp):
TTTCATAAAATAACGAGAAA
Found at i:3590385 original size:284 final size:282
Alignment explanation
Indices: 3590038--3590602 Score: 839
Period size: 284 Copynumber: 2.0 Consensus size: 282
3590028 ACTTTAGGCT
* *
3590038 TTAAAAAATGAAAAAAAAATTATGACTTATTTAATATTTTAATCATCATTTATAATAAACTTAAG
1 TTAAAAAATG-AAAAAAAATTAGGACTAATTTAATATTTTAATCATCATTTATAATAAACTTAAG
* * * * *
3590103 TGAGTATATTGTTAAATTTATATTTTGATTTCCATTGTCAATGTTTCATTGTTGATATAGCTTTT
65 TAAGTATATTGTTAAATTTAAATTTTGATTTCCATTGTCAATGTTTCATTGTTAATACAACTTTT
* * *
3590168 ATAACGATTTAATCACCAAA-AATTTTGAAATTTACTATAATAAATAAG-TTTATTAATTTTGTT
130 ATAACAATTTAATCA-CAAATAATTTAGAAATTCACTAT-ATAAAT-AGTTTTATTAATTTTGTT
* *
3590231 ATATGCTAAAATATCATGAGATAAGATTTAAATAAGCATGCAAAATTTATAAAAATAAGAAAAAA
192 ATATACTAAAATATCATGAGATAAGATTTAAATAAGCATACAAAATTTATAAAAA-AAGAAAAAA
*
3590296 GAATTCATTATTTTTTATAGAATTATA
256 GAATTCATTATTTTTTATAAAATTATA
* *
3590323 TTAAAAAATG-AAAAAAATTAGGGACTAATTTAATGTTTTAATCATCATTTATAATGAACTTAAG
1 TTAAAAAATGAAAAAAAATTA-GGACTAATTTAATATTTTAATCATCATTTATAATAAACTTAAG
* **
3590387 TAAGTATATTGTTAAATTTAAATTTTGATTTTCATTGTCTGTGTTTCATTGTTAATACAACTTTT
65 TAAGTATATTGTTAAATTTAAATTTTGATTTCCATTGTCAATGTTTCATTGTTAATACAACTTTT
* *
3590452 ATAACAATTTGATCACAAATAATTTAGAAATTCACTATATAAATTGTTTTATTAATTTTGTTATA
130 ATAACAATTTAATCACAAATAATTTAGAAATTCACTATATAAATAGTTTTATTAATTTTGTTATA
* * * *
3590517 TATTAAAGTATCATGAGATAATATTTATATAAGCATACAAAATTTATAAAAAAAGAAAAAAGAAT
195 TACTAAAATATCATGAGATAAGATTTAAATAAGCATACAAAATTTATAAAAAAAGAAAAAAGAAT
3590582 TCATTATTTTTTATAAAATTA
260 TCATTATTTTTTATAAAATTA
3590603 AAATTCTTTT
Statistics
Matches: 253, Mismatches: 24, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
282 34 0.13
283 84 0.33
284 125 0.49
285 10 0.04
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (282 bp):
TTAAAAAATGAAAAAAAATTAGGACTAATTTAATATTTTAATCATCATTTATAATAAACTTAAGT
AAGTATATTGTTAAATTTAAATTTTGATTTCCATTGTCAATGTTTCATTGTTAATACAACTTTTA
TAACAATTTAATCACAAATAATTTAGAAATTCACTATATAAATAGTTTTATTAATTTTGTTATAT
ACTAAAATATCATGAGATAAGATTTAAATAAGCATACAAAATTTATAAAAAAAGAAAAAAGAATT
CATTATTTTTTATAAAATTATA
Found at i:3591346 original size:24 final size:24
Alignment explanation
Indices: 3591309--3591356 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3591299 TCTTTTAGTT
3591309 ATGTATGAACACTCTGATTTGATC
1 ATGTATGAACACTCTGATTTGATC
*
3591333 ATGTATG-ACAACTCTTATTTGATC
1 ATGTATGAAC-ACTCTGATTTGATC
3591357 TCTAACAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (24 bp):
ATGTATGAACACTCTGATTTGATC
Found at i:3593077 original size:23 final size:26
Alignment explanation
Indices: 3593051--3593102 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 26
3593041 ATTTGATTAT
*
3593051 TTATTAGATAT-AAA-AAAA-TTTAA
1 TTATTAAATATAAAATAAAATTTTAA
3593074 TTATTAAATATAAAATAAAATTTTAA
1 TTATTAAATATAAAATAAAATTTTAA
3593100 TTA
1 TTA
3593103 ATATAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 10 0.40
24 3 0.12
25 4 0.16
26 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TTATTAAATATAAAATAAAATTTTAA
Found at i:3593115 original size:26 final size:25
Alignment explanation
Indices: 3593061--3593129 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 25
3593051 TTATTAGATA
*
3593061 TAAA-AAAATTTAATTATTAAATAT
1 TAAATAAAATTTAATTAATAAATAT
*
3593085 AAAATAAAATTTTAATTAATATAAT-T
1 TAAATAAAA-TTTAATTAATA-AATAT
3593111 TAAATATTAAA-TTAATTAA
1 TAAATA--AAATTTAATTAA
3593130 AATTTTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 3 0.08
25 4 0.11
26 24 0.65
27 3 0.08
28 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAATAAAATTTAATTAATAAATAT
Found at i:3593385 original size:20 final size:21
Alignment explanation
Indices: 3593342--3593406 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 21
3593332 AATAAAAGCA
*
3593342 TTTGAATAATATTT-AATATAAT
1 TTTG-ATAAT-TTTAAATATTAT
* *
3593364 TTTGATATTTTTATA-ATTA-
1 TTTGATAATTTTAAATATTAT
3593383 TTTGATAATTTTAAATATTAT
1 TTTGATAATTTTAAATATTAT
3593404 TTT
1 TTT
3593407 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 13 0.37
20 10 0.29
21 8 0.23
22 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTGATAATTTTAAATATTAT
Found at i:3593523 original size:8 final size:9
Alignment explanation
Indices: 3593502--3593550 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
3593492 TCTTAACATA
3593502 ATTTTT-AT
1 ATTTTTAAT
*
3593510 TTTTTTAAT
1 ATTTTTAAT
3593519 ATTTTTAAT
1 ATTTTTAAT
3593528 ATTAATTTAAT
1 ATT--TTTAAT
3593539 AATTTTTAAT
1 -ATTTTTAAT
3593549 AT
1 AT
3593551 AATTTTGGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 5 0.14
9 15 0.43
10 6 0.17
11 6 0.17
12 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:3593530 original size:20 final size:21
Alignment explanation
Indices: 3593513--3593555 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3593503 TTTTTATTTT
3593513 TTTAAT-ATTTTTAATATTAA
1 TTTAATAATTTTTAATATTAA
3593533 TTTAATAATTTTTAATA-TAA
1 TTTAATAATTTTTAATATTAA
3593553 TTT
1 TTT
3593556 TGGCGCCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATAATTTTTAATATTAA
Found at i:3598196 original size:13 final size:13
Alignment explanation
Indices: 3598178--3598202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3598168 TTATCTTGTA
3598178 ATGTAAAAATAAT
1 ATGTAAAAATAAT
3598191 ATGTAAAAATAA
1 ATGTAAAAATAA
3598203 AATTATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
ATGTAAAAATAAT
Found at i:3599232 original size:33 final size:36
Alignment explanation
Indices: 3599189--3599258 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
3599179 AAACTCATAA
3599189 TAAATATTAAT-ATCTAT-ATATTTATTAATTAATT
1 TAAATATTAATAATCTATAATATTTATTAATTAATT
*
3599223 TAAAT-TTAATAAATGTATACATATTTATTAATTAAT
1 TAAATATTAAT-AATCTATA-ATATTTATTAATTAAT
3599259 ACTTAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 5 0.16
34 5 0.16
35 5 0.16
37 16 0.52
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (36 bp):
TAAATATTAATAATCTATAATATTTATTAATTAATT
Found at i:3599265 original size:33 final size:33
Alignment explanation
Indices: 3599211--3599274 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3599201 TCTATATATT
*
3599211 TATTAATTAATTTAAATTTAATAAATGTATACA
1 TATTAATTAATTTAAACTTAATAAATGTATACA
* *
3599244 TATTTATTAA-TTAATACTTAATAAATTTATA
1 TATTAATTAATTTAA-ACTTAATAAATGTATA
3599275 AACCTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (33 bp):
TATTAATTAATTTAAACTTAATAAATGTATACA
Found at i:3600625 original size:43 final size:43
Alignment explanation
Indices: 3600564--3600688 Score: 214
Period size: 43 Copynumber: 2.9 Consensus size: 43
3600554 TCTGTCCTGT
3600564 TGATGCAACTTTGAGGATTTCTGACTTAGTAGTTGGATACGTC
1 TGATGCAACTTTGAGGATTTCTGACTTAGTAGTTGGATACGTC
3600607 TGATGCAACTTTGAGGATTTCTGACTTAGTAGTTGGATACGTC
1 TGATGCAACTTTGAGGATTTCTGACTTAGTAGTTGGATACGTC
* * * *
3600650 TGATGCAACTTTGAGGATTCCTAACTTAATAGCTGGATA
1 TGATGCAACTTTGAGGATTTCTGACTTAGTAGTTGGATA
3600689 TGTTTGAGTA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (43 bp):
TGATGCAACTTTGAGGATTTCTGACTTAGTAGTTGGATACGTC
Found at i:3603140 original size:15 final size:16
Alignment explanation
Indices: 3603120--3603149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3603110 AACCTTTTTA
3603120 TTTTTA-TTTTATAAT
1 TTTTTATTTTTATAAT
3603135 TTTTTATTTTTATAA
1 TTTTTATTTTTATAA
3603150 AAACAAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATTTTTATAAT
Found at i:3603456 original size:126 final size:119
Alignment explanation
Indices: 3603133--3603460 Score: 489
Period size: 119 Copynumber: 2.7 Consensus size: 119
3603123 TTATTTTATA
3603133 ATTTTTTATTTTTATAAAAACAAGACAATTAATATTTTAATTTATTAATGTAATTTTTTTAAATT
1 ATTTTTTATTTTTATAAAAACAAGACAATTAATATTTTAATTTATTAATGTAATTTTTTTAAATT
*
3603198 TAATTAAATATTATTTTTAATTTTATTAAAAAGTAATAATAATAAACTTTTTTT
66 TAATTAAATATTATTTTTAATCTTATTAAAAAGTAATAATAATAAACTTTTTTT
3603252 ATTTTTTATTTTTATAAAAACAAGACAATTAATATTTTAATTTATTAATGTAATTTTTTTAAATT
1 ATTTTTTATTTTTATAAAAACAAGACAATTAATATTTTAATTTATTAATGTAATTTTTTTAAATT
3603317 TAATTAAATATTATTTTTAATCTTATTAAAAAGTAATAATAATAAACTTTTTTT
66 TAATTAAATATTATTTTTAATCTTATTAAAAAGTAATAATAATAAACTTTTTTT
** * * *
3603371 ATTTTTTATTTAAATTTTTTTATTTTAAA-AA-ATAATTAATATTTTAATTTATTAATATAAATT
1 A---TTT-TTT--A--TTTTTA-TAAAAACAAGACAATTAATATTTTAATTTATTAATGTAATTT
* *
3603434 TTTTACACTTAATTAAATATTATTTTT
57 TTTTAAATTTAATTAAATATTATTTTT
3603461 TATTAAAAAT
Statistics
Matches: 192, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
119 119 0.62
122 3 0.02
123 3 0.02
125 1 0.01
126 54 0.28
127 8 0.04
128 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (119 bp):
ATTTTTTATTTTTATAAAAACAAGACAATTAATATTTTAATTTATTAATGTAATTTTTTTAAATT
TAATTAAATATTATTTTTAATCTTATTAAAAAGTAATAATAATAAACTTTTTTT
Found at i:3603491 original size:119 final size:119
Alignment explanation
Indices: 3603051--3603492 Score: 421
Period size: 119 Copynumber: 3.7 Consensus size: 119
3603041 AATTAAATAT
* * * * * *
3603051 TATTTTAGTTTGTTAATATAAATTTTTTAAACTTAATTAAATATTA-TTTTTTAATAAAAA--AC
1 TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTTTATTAAAAAGTA-
* * * * *
3603113 CT--T-TTTATT-TTTATTTTATAATTTTTTATTTTTATAAAAACAAGACAATTAA
65 ATAATAATAATTATTTATTTT-TTATTTATTATTTTTATAAAAACAAGACAATTAA
3603165 TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTAATTTTATTAAAAA
1 TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTA--TTT--TTTTATTAAAAA
* *
3603230 GTAATAATAATAA--A-CT-TTTTTTATTTTTTATTTTTATAAAAACAAGACAATTAA
62 GTAATAATAATAATTATTTATTTTTTATTTATTATTTTTATAAAAACAAGACAATTAA
3603284 TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTAATCTTATTAAAAA
1 TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTA-TTTT--T-TTATTAAAAA
* ** *
3603349 GTAATAATAATAAACTTTTTTTATTTTTTATTTAAATT-TTTTTATTTTAAA-AA-ATAATTAA
62 GTAATAATAAT-AA--TTATTTATTTTTTATTT--ATTATTTTTA-TAAAAACAAGACAATTAA
* * * *
3603410 TATTTTAATTTATTAATATAAATTTTTTACACTTAATTAAATATTA-TTTTTTATTAAAAA-TAA
1 TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTTTATTAAAAAGTAA
3603473 TAATTAATATATTATTTATT
66 TAA-TAATA-ATTATTTATT
3603493 AAATTTTTTA
Statistics
Matches: 280, Mismatches: 22, Indels: 47
0.80 0.06 0.13
Matches are distributed among these distances:
114 41 0.15
116 1 0.00
117 2 0.01
118 5 0.02
119 119 0.43
120 14 0.05
121 17 0.06
122 2 0.01
123 2 0.01
124 3 0.01
125 1 0.00
126 59 0.21
127 8 0.03
128 6 0.02
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (119 bp):
TATTTTAATTTATTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTTTATTAAAAAGTAA
TAATAATAATTATTTATTTTTTATTTATTATTTTTATAAAAACAAGACAATTAA
Found at i:3605884 original size:2 final size:2
Alignment explanation
Indices: 3605879--3605916 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3605869 ACACACACAC
3605879 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
3605917 CTTGTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3612005 original size:344 final size:343
Alignment explanation
Indices: 3611363--3612018 Score: 1046
Period size: 344 Copynumber: 1.9 Consensus size: 343
3611353 GTGGCTACAG
* * * *
3611363 TAGGTTTTTTGGGATAGAGGTTGTCAGGGTGCCTAAAGATCTGGCAATGGTTGCATCTTTGAGGT
1 TAGGTTTTTTGGGATAGAGGTTGTCAAGGTGCCCAAAGATCTGGCAACGGCTGCATCTTTGAGGT
* * **
3611428 ATCCATGGAATATCTACTAAAACTGATGTAATGGTGTCGTCGTTTACTTCAACCTCAATTGTGCT
66 ATCCACGAAATATCTACTAAAACTGATGTAATGGTGTCGTCCATTACTTCAACCTCAATTGTGCT
* *
3611493 TGGAATCTCTTAGCAAGCACTAATTTTAGCACAAACTTTTGCAAATTCTAAGCATTGCTGGGAAG
131 TAGAATCTCTTAGCAAGCACTAATTTTAACACAAACTTTTGCAAATTCTAAGCATTGCTGGGAAG
* **
3611558 CTGTAATGTGGTCCATATATATAAGGCTCCCTTAAACGCTCGTTATGTAACTCAAACCATTCTTG
196 CTGTAATATGGTCCATATATATAAGGCTCCCTTAAACGCTCGCCATGTAACTCAAACCATTCTTG
* *
3611623 GTGTAAAGCTCGAGTGGAATTTTGCTCAAAAAGATCCAAACAAGGGAGTTTTTTGGGATTCTACT
261 ATGTAAAGCTCGAGTGGAATTCTGCTCAAAAAGATCCAAACAA-GGAGTTTTTTGGGATTCTACT
3611688 CGAGTGGAATTCTGCTCAA
325 CGAGTGGAATTCTGCTCAA
3611707 TAGGTTTTTTGGGATAGAGGTTGTCAAGGTGCCCAAAGATCTGGCAACGGCTGCATCTTTGAGGT
1 TAGGTTTTTTGGGATAGAGGTTGTCAAGGTGCCCAAAGATCTGGCAACGGCTGCATCTTTGAGGT
* *
3611772 ATCCACGAAATATCTACTGAAACT-ACTGTAATGGTGTCGTCCATTAGTTCAACCTCAATTGTGC
66 ATCCACGAAATATCTACTAAAACTGA-TGTAATGGTGTCGTCCATTACTTCAACCTCAATTGTGC
* *
3611836 TTAGAATCTCTTGGCAAGCACTAATTTTAACACAAACTTTTGCAAATTCTAAGCGTTGCTGGGAA
130 TTAGAATCTCTTAGCAAGCACTAATTTTAACACAAACTTTTGCAAATTCTAAGCATTGCTGGGAA
* * * *
3611901 GCTGTAATATGGTCCATATATATAGGGCTCCC-TAAAGTGCTCGCCATGTAATTCAAACCATTTT
195 GCTGTAATATGGTCCATATATATAAGGCTCCCTTAAA-CGCTCGCCATGTAACTCAAACCATTCT
* *
3611965 TGATGTAAAGCTCGAGTGGAATTCTGCTCAGAAGGATCCAAACAAGGAGTTTTT
259 TGATGTAAAGCTCGAGTGGAATTCTGCTCAAAAAGATCCAAACAAGGAGTTTTT
3612019 CCATACTGAA
Statistics
Matches: 285, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
343 14 0.05
344 271 0.95
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (343 bp):
TAGGTTTTTTGGGATAGAGGTTGTCAAGGTGCCCAAAGATCTGGCAACGGCTGCATCTTTGAGGT
ATCCACGAAATATCTACTAAAACTGATGTAATGGTGTCGTCCATTACTTCAACCTCAATTGTGCT
TAGAATCTCTTAGCAAGCACTAATTTTAACACAAACTTTTGCAAATTCTAAGCATTGCTGGGAAG
CTGTAATATGGTCCATATATATAAGGCTCCCTTAAACGCTCGCCATGTAACTCAAACCATTCTTG
ATGTAAAGCTCGAGTGGAATTCTGCTCAAAAAGATCCAAACAAGGAGTTTTTTGGGATTCTACTC
GAGTGGAATTCTGCTCAA
Found at i:3616854 original size:67 final size:68
Alignment explanation
Indices: 3616709--3617130 Score: 240
Period size: 67 Copynumber: 6.3 Consensus size: 68
3616699 TTTCACATAA
* * * * *
3616709 GGAGAAGTCGACCATTGTGGTCCAATGCACCACTTCCGTCACTCTATC-ATATACAAG--TTCTT
1 GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAGTATTCTT
3616771 GCAAT
66 --AAT
** * * * *
3616776 TCAAAATTCGACCGTTGTGGTCCCATGCGCCACTTCCATCAATCACTCTA-ATACAAGTATTCTT
1 GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAGTATTCTT
3616840 AAT
66 AAT
* * * * * * *
3616843 GGAGAAGTCGACCATTATAGT-CCATGTGCCACTTCTATCACTTTC-CTATATATAAG--TTCTT
1 GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAGTATTCTT
3616904 CCAAT
66 --AAT
** * * * * * * * * *
3616909 GGAGAAGTTAACTGTGGTGGTCCCACGTGCCATTTCCGTCATTCTCCCTA-ATACAATTATTCTT
1 GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAGTATTCTT
3616973 AAT
66 AAT
* ** ** * *** * *
3616976 -GAAAAGTCGACCGTTGTGGTCTTATATGCCATTTTTTTCACTCT-TTTATATACAAGTTCTTC-
1 GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAG-TATTCT
*
3617038 TAGT
65 TAAT
* * * * * * * * *
3617042 AGATAAGTCAACCTTTGTTGTCACATGCACCACTTCCATCATTCTCTCTA-ATATAAGTATTCTT
1 GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAGTATTCTT
3617106 AAT
66 AAT
* *
3617109 AGAGAAGTCGACCGTTATGGTC
1 GGAGAAGTCGACCGTTGTGGTC
3617131 TTATTTTCCA
Statistics
Matches: 260, Mismatches: 80, Indels: 30
0.70 0.22 0.08
Matches are distributed among these distances:
64 5 0.02
65 5 0.02
66 86 0.33
67 147 0.57
68 7 0.03
69 10 0.04
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (68 bp):
GGAGAAGTCGACCGTTGTGGTCCCATGCGCCACTTCCATCACTCTCTCTATATACAAGTATTCTT
AAT
Found at i:3616929 original size:133 final size:133
Alignment explanation
Indices: 3616738--3617131 Score: 357
Period size: 133 Copynumber: 3.0 Consensus size: 133
3616728 GTCCAATGCA
** * ** * * *
3616738 CCACTTCCGTCACTCTATC-ATATACAAGTTCTTGCAATTCAAAATTCGACCGTT-GTGGTCCCA
1 CCACTTCTATCACTCT-TCTATATACAAGTTCTTCCAATAGAGAAGTCAACC-TTGGTGGTCCCA
* * *
3616801 TGCGCCACTTCCATCAATCACTCTAATACAAGTATTCTTAATGGAGAAGTCGACCATTATAGTC-
64 TGCGCCACTTCCATCATTCTCTCTAATACAAGTATTCTTAAT-GAGAAGTCGACCGTTATAGTCT
*
3616865 CATGTG
128 CATATG
* * *
3616871 CCACTTCTATCACT-TTCCTATATATAAGTTCTTCCAATGGAGAAGTTAA-CTGTGGTGGTCCCA
1 CCACTTCTATCACTCTT-CTATATACAAGTTCTTCCAATAGAGAAGTCAACCT-TGGTGGTCCCA
* * * * * * * * * *
3616934 CGTGCCATTTCCGTCATTCTCCCTAATACAATTATTCTTAATGAAAAGTCGACCGTTGTGGTCTT
64 TGCGCCACTTCCATCATTCTCTCTAATACAAGTATTCTTAATGAGAAGTCGACCGTTATAGTCTC
3616999 ATATG
129 ATATG
* * * * * * * * * *
3617004 CCATTTTTTTCACTCTTTTATATACAAGTTCTTCTAGTAGATAAGTCAACCTTTGTTGTCACATG
1 CCACTTCTATCACTCTTCTATATACAAGTTCTTCCAATAGAGAAGTCAACCTTGGTGGTCCCATG
* * *
3617069 CACCACTTCCATCATTCTCTCTAATATAAGTATTCTTAATAGAGAAGTCGACCGTTATGGTCT
66 CGCCACTTCCATCATTCTCTCTAATACAAGTATTCTTAAT-GAGAAGTCGACCGTTATAGTCT
3617132 TATTTTCCAT
Statistics
Matches: 206, Mismatches: 47, Indels: 15
0.77 0.18 0.06
Matches are distributed among these distances:
131 2 0.01
132 21 0.10
133 159 0.77
134 24 0.12
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (133 bp):
CCACTTCTATCACTCTTCTATATACAAGTTCTTCCAATAGAGAAGTCAACCTTGGTGGTCCCATG
CGCCACTTCCATCATTCTCTCTAATACAAGTATTCTTAATGAGAAGTCGACCGTTATAGTCTCAT
ATG
Found at i:3618080 original size:20 final size:20
Alignment explanation
Indices: 3618055--3618131 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
3618045 AAGTACGCAG
3618055 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
3618075 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
3618095 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
3618115 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
3618132 GTCTTTTTAC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3621524 original size:29 final size:29
Alignment explanation
Indices: 3621472--3621539 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
3621462 TTTTTAACAT
* * * *
3621472 AAGTACTTTTGGCACAGATGCTTTGATAC
1 AAGTACTTTTGACACAAATACTTTAATAC
*
3621501 AAGTACTTTTGACATAAATACTTTAATAC
1 AAGTACTTTTGACACAAATACTTTAATAC
* *
3621530 AGGTATTTTT
1 AAGTACTTTT
3621540 AGTACAAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (29 bp):
AAGTACTTTTGACACAAATACTTTAATAC
Found at i:3622329 original size:6 final size:7
Alignment explanation
Indices: 3622312--3622442 Score: 70
Period size: 6 Copynumber: 20.0 Consensus size: 7
3622302 TTATGTTAAG
3622312 TTATATA
1 TTATATA
3622319 TTATA-A
1 TTATATA
3622325 TTATAT-
1 TTATATA
*
3622331 TTAAAATA
1 TT-ATATA
3622339 TTATATA
1 TTATATA
3622346 TT-TATA
1 TTATATA
3622352 TT-T-T-
1 TTATATA
3622356 TTATATA
1 TTATATA
3622363 TTA-ATAA
1 TTATAT-A
*
3622370 TT-TAAA
1 TTATATA
3622376 TTATATA
1 TTATATA
* *
3622383 -AATTTA
1 TTATATA
*
3622389 ATATAT-
1 TTATATA
3622395 TTATATA
1 TTATATA
3622402 TT-TATA
1 TTATATA
3622408 TTATAT-
1 TTATATA
*
3622414 TCATATA
1 TTATATA
*
3622421 TTTTTATA
1 -TTATATA
* *
3622429 TCATATT
1 TTATATA
3622436 TTATATA
1 TTATATA
3622443 ATATTTTAAT
Statistics
Matches: 93, Mismatches: 17, Indels: 28
0.67 0.12 0.20
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
6 41 0.44
7 41 0.44
8 7 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:3622361 original size:17 final size:18
Alignment explanation
Indices: 3622339--3622479 Score: 78
Period size: 17 Copynumber: 7.6 Consensus size: 18
3622329 ATTTAAAATA
3622339 TTATATATTTATATTT-T
1 TTATATATTTATATTTAT
*
3622356 TTATATATTAATAATTTAAAT
1 TTATATATTTAT-ATTT--AT
* *
3622377 TATATAAATTTA-ATATAT
1 T-TATATATTTATATTTAT
3622395 TTATATATTTATATTATAT
1 TTATATATTTATATT-TAT
* *
3622414 TCATATATTTTTATATCATAT
1 T--TATATATTTATAT-TTAT
* *
3622435 TT-TATA-TAATATTTTAA
1 TTATATATTTATA-TTTAT
3622452 TTATAT-TTT-TATTTAT
1 TTATATATTTATATTTAT
3622468 GTTCATATATTT
1 -TT-ATATATTT
3622480 CTTGATTTCC
Statistics
Matches: 94, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
16 4 0.04
17 32 0.34
18 21 0.22
19 8 0.09
20 3 0.03
21 18 0.19
22 8 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATATATTTATATTTAT
Found at i:3622399 original size:39 final size:38
Alignment explanation
Indices: 3622313--3622457 Score: 122
Period size: 39 Copynumber: 3.8 Consensus size: 38
3622303 TATGTTAAGT
*
3622313 TATATATTATA-ATT-ATATTTAAAATATTATATATTT-A
1 TATAT-TTATATATTAATATTTAAATTA-TATATATTTAA
* *
3622350 TATTTTTTATATATTAATAATTTAAATTATATAAATTTAA
1 TA-TATTTATATATTAAT-ATTTAAATTATATATATTTAA
* * *
3622390 TATATTTATATATTTATA-TTATATTCATATATTTTTATA
1 TATATTTATATATTAATATTTAAATT-ATATATATTTA-A
*
3622429 TCATATTT-TATA-TAATATTTTAATTATAT
1 T-ATATTTATATATTAATATTTAAATTATAT
3622458 TTTTATTTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
37 13 0.15
38 23 0.26
39 34 0.39
40 18 0.20
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (38 bp):
TATATTTATATATTAATATTTAAATTATATATATTTAA
Found at i:3622461 original size:12 final size:12
Alignment explanation
Indices: 3622390--3622464 Score: 70
Period size: 11 Copynumber: 6.5 Consensus size: 12
3622380 ATAAATTTAA
3622390 TATATTTATATATT
1 TATA-TTATAT-TT
3622404 TATATTATA-TT
1 TATATTATATTT
*
3622415 CATA-TAT-TTT
1 TATATTATATTT
*
3622425 TATATCATATTT
1 TATATTATATTT
*
3622437 TATATAATATTT
1 TATATTATATTT
3622449 TA-ATTATATTT
1 TATATTATATTT
3622460 T-TATT
1 TATATT
3622465 TATGTTCATA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
10 8 0.15
11 19 0.37
12 16 0.31
13 5 0.10
14 4 0.08
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATTATATTT
Found at i:3622625 original size:6 final size:6
Alignment explanation
Indices: 3622614--3622644 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3622604 TGATCTTTTA
3622614 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
3622645 GTATAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:3623538 original size:2 final size:2
Alignment explanation
Indices: 3623533--3623557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3623523 TGTGAGAGAT
3623533 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
3623558 GTGTGTGTGA
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:3623990 original size:3 final size:3
Alignment explanation
Indices: 3623982--3624017 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3623972 ATTTATTCAT
3623982 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3624018 ATTGGCAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3630344 original size:97 final size:98
Alignment explanation
Indices: 3630153--3630346 Score: 293
Period size: 97 Copynumber: 2.0 Consensus size: 98
3630143 ACTAAATGAC
* * * *
3630153 AACTTCATAAAACTAGTAATATCAGAACTTCATCGTCTCTTTTTTTTTTAGTTTTTAGCTTAATC
1 AACTTCATAAAACTAATAATATCAAAACTTCATCGTCTC-TTTTTTTTAAGTTTTGAGCTTAATC
*
3630218 TAATTAATTTATATAATTATTTTTAAAATATAAT
65 CAATTAATTTATATAATTATTTTTAAAATATAAT
* *
3630252 AACTTCATAAAACTAATAATATTAAAACTTCATCGTCTC-TTTTTTTAAGTTTTCGA-CTTGATC
1 AACTTCATAAAACTAATAATATCAAAACTTCATCGTCTCTTTTTTTTAAGTTTT-GAGCTTAATC
3630315 CAATTAATTTATATAATTATTTTTAAAATATA
65 CAATTAATTTATATAATTATTTTTAAAATATA
3630347 CATCAAATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
97 50 0.57
98 1 0.01
99 36 0.41
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (98 bp):
AACTTCATAAAACTAATAATATCAAAACTTCATCGTCTCTTTTTTTTAAGTTTTGAGCTTAATCC
AATTAATTTATATAATTATTTTTAAAATATAAT
Found at i:3632197 original size:24 final size:26
Alignment explanation
Indices: 3632150--3632199 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3632140 TATTTATTAT
**
3632150 TAAAAAATATATAAATGATTGATAAA
1 TAAAAAATATATAAATGAAAGATAAA
3632176 TAAAAAATAT-TAAAT-AAAGATAAA
1 TAAAAAATATATAAATGAAAGATAAA
3632200 AATTAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (26 bp):
TAAAAAATATATAAATGAAAGATAAA
Found at i:3632700 original size:16 final size:17
Alignment explanation
Indices: 3632681--3632721 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3632671 TTATAAATTT
3632681 TTATTATTAATCAAA-A
1 TTATTATTAATCAAATA
*
3632697 TTATTAATTTATCAAATA
1 TTATT-ATTAATCAAATA
3632715 TT-TTATT
1 TTATTATT
3632722 TATAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 11 0.50
18 3 0.14
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTATTAATCAAATA
Found at i:3632712 original size:17 final size:17
Alignment explanation
Indices: 3632681--3632724 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3632671 TTATAAATTT
*
3632681 TTATTATTAATCAAA-A
1 TTATTATTTATCAAATA
3632697 TTATTAATTTATCAAATA
1 TTATT-ATTTATCAAATA
3632715 TT-TTATTTAT
1 TTATTATTTAT
3632725 AGAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 11 0.44
17 11 0.44
18 3 0.12
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTATTTATCAAATA
Found at i:3633283 original size:15 final size:16
Alignment explanation
Indices: 3633252--3633313 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
3633242 GTTGACTTTG
3633252 AATTTAAATTATTTTA
1 AATTTAAATTATTTTA
3633268 AATTTAAATT-TTTTA
1 AATTTAAATTATTTTA
*
3633283 AATTTAATTTATTTTA
1 AATTTAAATTATTTTA
* * *
3633299 AGTTCAAGTTATTTT
1 AATTTAAATTATTTT
3633314 TGACCTGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 14 0.34
16 27 0.66
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:3635685 original size:28 final size:28
Alignment explanation
Indices: 3635641--3635694 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
3635631 TCGATGATTA
3635641 GAAAAAATCGGGATTGGAGTATCCCTTC
1 GAAAAAATCGGGATTGGAGTATCCCTTC
*
3635669 GAAAATAA-CGGGGTTGGAGTATCCCT
1 GAAAA-AATCGGGATTGGAGTATCCCT
3635695 AATTATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (28 bp):
GAAAAAATCGGGATTGGAGTATCCCTTC
Found at i:3635704 original size:76 final size:78
Alignment explanation
Indices: 3635573--3635773 Score: 212
Period size: 76 Copynumber: 2.6 Consensus size: 78
3635563 GAGATAATAA
* * ** * *
3635573 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-
*
3635637 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* *
3635649 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
* *
3635714 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * * *
3635728 CGGGGTTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
3635774 GATGAAATAA
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
75 7 0.07
76 48 0.47
77 2 0.02
78 3 0.03
79 43 0.42
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:3635790 original size:28 final size:28
Alignment explanation
Indices: 3635731--3635804 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3635721 ATAAAGCCGG
*** * * *
3635731 GGTTGGAGTATCCCCTCGGAAGTAATGG
1 GGTTGGAGTATCCCCGATGAAATAACGA
3635759 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGATGAAATAACGA
*
3635787 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCCCGAT
3635805 TGTGAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:3635857 original size:52 final size:50
Alignment explanation
Indices: 3635788--3635957 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
3635778 AAATAACGAG
* * *
3635788 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
3635840 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
3635893 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
3635944 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
3635958 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:3635976 original size:28 final size:28
Alignment explanation
Indices: 3635931--3636012 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
3635921 AGTGTTTTAA
* *
3635931 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
3635958 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
3635985 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
3636013 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:3638453 original size:13 final size:13
Alignment explanation
Indices: 3638435--3638460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3638425 ACAAAGATCC
3638435 ATGTATCGATACA
1 ATGTATCGATACA
3638448 ATGTATCGATACA
1 ATGTATCGATACA
3638461 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3638456 original size:33 final size:33
Alignment explanation
Indices: 3638414--3638479 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3638404 AAAATTTCCA
***
3638414 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3638447 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3638480 CTTTCCTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3638524 original size:19 final size:18
Alignment explanation
Indices: 3638500--3638567 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3638490 CAGTAGCTAA
3638500 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3638519 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3638534 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3638551 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3638568 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3638540 original size:13 final size:13
Alignment explanation
Indices: 3638522--3638546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3638512 ACAATACTTA
3638522 TGTATCGATACAT
1 TGTATCGATACAT
3638535 TGTATCGATACA
1 TGTATCGATACA
3638547 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3638544 original size:32 final size:32
Alignment explanation
Indices: 3638503--3638565 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3638493 TAGCTAATTA
*
3638503 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3638535 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3638566 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3638677 original size:19 final size:19
Alignment explanation
Indices: 3638653--3638692 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3638643 GATACATTTA
3638653 AATTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTC
3638672 AATTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTC
3638691 AA
1 AA
3638693 ACACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (19 bp):
AATTTTTTTTTTTTTTTTC
Found at i:3640179 original size:13 final size:14
Alignment explanation
Indices: 3640144--3640197 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 14
3640134 GATATTTTTT
3640144 ATATAATATAAAAA
1 ATATAATATAAAAA
*
3640158 ATTAAAATATAAAAA
1 A-TATAATATAAAAA
* *
3640173 A-ATAATATAATAT
1 ATATAATATAAAAA
*
3640186 ATATGATATAAA
1 ATATAATATAAA
3640198 TATATAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 10 0.31
14 9 0.28
15 13 0.41
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
ATATAATATAAAAA
Found at i:3642003 original size:13 final size:13
Alignment explanation
Indices: 3641962--3642014 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
3641952 GCCGTTGGGC
3641962 ACAATGTATCGAT
1 ACAATGTATCGAT
3641975 AC-AT-T-TC-AT
1 ACAATGTATCGAT
3641984 -C-ATGTATCGAT
1 ACAATGTATCGAT
*
3641995 ACAATGTATTGAT
1 ACAATGTATCGAT
3642008 ACAATGT
1 ACAATGT
3642015 CCCATGTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 3 0.09
9 3 0.09
10 4 0.12
11 3 0.09
12 3 0.09
13 18 0.53
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:3642009 original size:33 final size:33
Alignment explanation
Indices: 3641962--3642030 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3641952 GCCGTTGGGC
* *
3641962 ACAATGTATCGATAC-ATTTCATCATGTATCGAT
1 ACAATGTATCGATACAATGTC-CCATGTATCGAT
*
3641995 ACAATGTATTGATACAATGTCCCATGTATCGAT
1 ACAATGTATCGATACAATGTCCCATGTATCGAT
3642028 ACA
1 ACA
3642031 TTTCACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTCCCATGTATCGAT
Found at i:3642102 original size:19 final size:19
Alignment explanation
Indices: 3642075--3642114 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3642065 TCAATATAAT
*
3642075 TGAGTATGTATCGATACAA
1 TGAGCATGTATCGATACAA
3642094 TGAGCATGTATCGATACAA
1 TGAGCATGTATCGATACAA
3642113 TG
1 TG
3642115 TATCGATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (19 bp):
TGAGCATGTATCGATACAA
Found at i:3642117 original size:13 final size:13
Alignment explanation
Indices: 3642099--3642130 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3642089 TACAATGAGC
3642099 ATGTATCGATACA
1 ATGTATCGATACA
3642112 ATGTATCGATACA
1 ATGTATCGATACA
*
3642125 AAGTAT
1 ATGTAT
3642131 AATGTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3644752 original size:20 final size:21
Alignment explanation
Indices: 3644722--3644760 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3644712 TCTGAGTTTT
3644722 TTCAGATGTATCGATACATCA
1 TTCAGATGTATCGATACATCA
3644743 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCGATACAT
3644761 TCTGGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCA
Found at i:3652086 original size:3 final size:3
Alignment explanation
Indices: 3652078--3652104 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3652068 TTATATTTTC
3652078 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3652105 TAACAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3653085 original size:5 final size:5
Alignment explanation
Indices: 3653075--3653116 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
3653065 AAACTCAAAA
3653075 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
3653117 TTATTATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:3654393 original size:5 final size:5
Alignment explanation
Indices: 3654383--3654414 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3654373 TAAAATATAA
3654383 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
3654415 CATTCATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:3654588 original size:4 final size:4
Alignment explanation
Indices: 3654581--3654617 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
3654571 GTCATTCATA
3654581 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
3654618 AAAATAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:3656139 original size:2 final size:2
Alignment explanation
Indices: 3656132--3656164 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3656122 CAATTTTTAA
3656132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3656165 CTATTTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3656585 original size:19 final size:17
Alignment explanation
Indices: 3656548--3656598 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3656538 TTAATTGTAT
*
3656548 AAATA-TAAATATAAAAA
1 AAATATTAAATAT-ATAA
*
3656565 AAATAATTAAATATATGA
1 AAAT-ATTAAATATATAA
*
3656583 AAATTTTAAATATATA
1 AAATATTAAATATATA
3656599 TATAATACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.50
18 7 0.25
19 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATATTAAATATATAA
Found at i:3656682 original size:20 final size:21
Alignment explanation
Indices: 3656659--3656698 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
3656649 ATATATCATG
3656659 TTATGTTTATTATA-ATATTT
1 TTATGTTTATTATATATATTT
3656679 TTATGTTTATTATATATATT
1 TTATGTTTATTATATATATT
3656699 GTGTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TTATGTTTATTATATATATTT
Found at i:3656830 original size:2 final size:2
Alignment explanation
Indices: 3656823--3656864 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3656813 CATTATCCTC
3656823 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
3656865 CAGAGGATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3657172 original size:20 final size:20
Alignment explanation
Indices: 3657132--3657169 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3657122 TAAATCGATC
*
3657132 TAATTAAAATTAATATTTTA
1 TAATTAAAATAAATATTTTA
3657152 TAATTAAAA-AAATATTTT
1 TAATTAAAATAAATATTTT
3657170 TATTTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTAAAATAAATATTTTA
Found at i:3657327 original size:82 final size:82
Alignment explanation
Indices: 3657153--3657330 Score: 200
Period size: 82 Copynumber: 2.1 Consensus size: 82
3657143 AATATTTTAT
**
3657153 AATTAAAAAAATATTTTTATTTAAGTTATTATAAAATATATATATATATTAATAGTAAAAATCAA
1 AATT-AAAAAATATTTTTATTTAAGTTATTATAAAATATATATATATATTAATAACAAAAATCAA
* *** ** *
3657218 TTAAAATTGATATTTTAT
65 ATAAAACAAATAGGTTAG
3657236 AATTAAAAAATATTTTTATTTAAGTTATTATAAACTATATATATTAATATATTAATAACAAAAAT
1 AATTAAAAAATATTTTTATTTAAGTTATTATAAA--ATATATA-T-ATATATTAATAACAAAAAT
*
3657301 -AAATAAGACAAATAGGTT-G
62 CAAATAAAACAAATAGGTTAG
3657320 AA-TAAAAAATA
1 AATTAAAAAATA
3657331 AATTTAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
82 30 0.37
83 13 0.16
84 9 0.11
85 12 0.15
86 17 0.21
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (82 bp):
AATTAAAAAATATTTTTATTTAAGTTATTATAAAATATATATATATATTAATAACAAAAATCAAA
TAAAACAAATAGGTTAG
Found at i:3657423 original size:2 final size:2
Alignment explanation
Indices: 3657416--3657441 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3657406 ATATTAAAGC
3657416 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
3657442 TTGAAGAACC
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:3658204 original size:26 final size:27
Alignment explanation
Indices: 3658163--3658213 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
3658153 GGATTAATCA
3658163 GCTTCCGAAGTGTTAACTATAAGAGGT
1 GCTTCCGAAGTGTTAACTATAAGAGGT
* *
3658190 GCTTCC-AATTGTTAACTGTAAGAG
1 GCTTCCGAAGTGTTAACTATAAGAG
3658214 CTGAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (27 bp):
GCTTCCGAAGTGTTAACTATAAGAGGT
Found at i:3667571 original size:13 final size:13
Alignment explanation
Indices: 3667555--3667595 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
3667545 ATTATTATAT
3667555 AATTATATTAATA
1 AATTATATTAATA
3667568 AATTATTATTAATAA
1 AATTA-TATTAAT-A
3667583 AATTA-ATTAATA
1 AATTATATTAATA
3667595 A
1 A
3667596 TAAATCTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.08
13 11 0.42
14 7 0.27
15 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATATTAATA
Found at i:3668341 original size:2 final size:2
Alignment explanation
Indices: 3668293--3668327 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3668283 TCAACTCTGT
3668293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3668328 CGTGTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3670041 original size:2 final size:2
Alignment explanation
Indices: 3670034--3670064 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3670024 TAAAATATTT
3670034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3670065 GTGTGTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3670179 original size:16 final size:17
Alignment explanation
Indices: 3670147--3670180 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3670137 ACATTTGCTT
*
3670147 TATTTAGTATTATTTTA
1 TATTTAGTATTAGTTTA
3670164 TATTTA-TATTAGTTTA
1 TATTTAGTATTAGTTTA
3670180 T
1 T
3670181 TTATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTAGTATTAGTTTA
Found at i:3670454 original size:15 final size:16
Alignment explanation
Indices: 3670436--3670467 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3670426 AATAAAATTA
3670436 TTATATAAAT-TTTAT
1 TTATATAAATATTTAT
3670451 TTATATAAATATTTAT
1 TTATATAAATATTTAT
3670467 T
1 T
3670468 AATTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATAAATATTTAT
Found at i:3670739 original size:16 final size:17
Alignment explanation
Indices: 3670720--3670764 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
3670710 ATTTGAACTC
*
3670720 AAAATAATCTGAATAT-
1 AAAATAATCTAAATATA
* *
3670736 AAAATAATTTAAATTTA
1 AAAATAATCTAAATATA
3670753 AAAATAATCTAA
1 AAAATAATCTAA
3670765 TCCGAACTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATAATCTAAATATA
Found at i:3671598 original size:16 final size:16
Alignment explanation
Indices: 3671548--3671603 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
3671538 CAAACAGTAC
*
3671548 TTTTACAAATATTAATA
1 TTTTA-AAATAATAATA
* *
3671565 TTTTAAATTAAT-ACA
1 TTTTAAAATAATAATA
3671580 TTTTAAAATAATAATA
1 TTTTAAAATAATAATA
3671596 TTTTAAAA
1 TTTTAAAA
3671604 ATTCTTCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 13 0.39
16 15 0.45
17 5 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTTAAAATAATAATA
Found at i:3685522 original size:3 final size:3
Alignment explanation
Indices: 3685507--3685536 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3685497 TTAATTAATG
*
3685507 ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3685537 TTCATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3685852 original size:31 final size:31
Alignment explanation
Indices: 3685758--3685853 Score: 96
Period size: 28 Copynumber: 3.3 Consensus size: 31
3685748 AGTTTATTTT
*
3685758 TATTTAAATTATT-TTTTAAATAAT-AAA-AA
1 TATTTTAA-TATTATTTTAAATAATAAAATAA
* *
3685787 TATTTAAATA-TATATT-AAT-ATAAAATAA
1 TATTTTAATATTATTTTAAATAATAAAATAA
*
3685815 AATTTTAATATTATTTTAAATAATAAAATAA
1 TATTTTAATATTATTTTAAATAATAAAATAA
*
3685846 TTTTTTAA
1 TATTTTAA
3685854 ATAAATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
26 2 0.04
27 7 0.13
28 15 0.27
29 13 0.24
30 3 0.05
31 15 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TATTTTAATATTATTTTAAATAATAAAATAA
Found at i:3686005 original size:3 final size:3
Alignment explanation
Indices: 3685997--3686032 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3685987 ATGGAAATGC
3685997 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3686033 AAAAGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.