Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 146 of 168
Found at i:42955759 original size:21 final size:21
Alignment explanation
Indices: 42955733--42955772 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42955723 TATACGAGTA
42955733 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTTAATAC
42955754 AATTTACATTCAATTTAAT
1 AATTTACATTCAATTTAAT
42955773 CCAAGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:42955783 original size:21 final size:21
Alignment explanation
Indices: 42955742--42955783 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42955732 AAATTTAACA
* *
42955742 TCAATTTAATACAATTTACAT
1 TCAATTTAATACAAGTCACAT
*
42955763 TCAATTTAATCCAAGTCACAT
1 TCAATTTAATACAAGTCACAT
42955784 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (21 bp):
TCAATTTAATACAAGTCACAT
Found at i:42957430 original size:31 final size:31
Alignment explanation
Indices: 42957350--42957430 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
42957340 AGTAATATAT
*
42957350 AATTTAAATTTATTA-TTATATATTTTTTGAA
1 AATTT-AATTTATTATTTATATATCTTTTGAA
*
42957381 AATATTAATGTATT-TTTATATA-CTTTT-AA
1 AAT-TTAATTTATTATTTATATATCTTTTGAA
42957410 AATTTATATATTATTATTTAT
1 AATTTA-AT-TTATTATTTAT
42957431 TGTCAACAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
28 3 0.07
29 7 0.17
30 8 0.19
31 22 0.52
32 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (31 bp):
AATTTAATTTATTATTTATATATCTTTTGAA
Found at i:42957476 original size:50 final size:50
Alignment explanation
Indices: 42957419--42957514 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
42957409 AAATTTATAT
* *
42957419 ATTATTATT-TATTGTCAACAATATTT-TTTATTTTATATATTTTTTAAAAA
1 ATTATTATTATATTGTCAAAAATATTTATGTATTTT-T-TATTTTTTAAAAA
* *
42957469 ATTATTATTATATTTTTAAAAATATTTATGTATTTTTTATTTTTTA
1 ATTATTATTATATTGTCAAAAATATTTATGTATTTTTTATTTTTTA
42957515 GAATTAGGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 18 0.45
51 15 0.38
52 7 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (50 bp):
ATTATTATTATATTGTCAAAAATATTTATGTATTTTTTATTTTTTAAAAA
Found at i:42957489 original size:21 final size:22
Alignment explanation
Indices: 42957450--42957507 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
42957440 TATTTTTTAT
*
42957450 TTTATATAT-TTTTTAAAAA-A
1 TTTATGTATATTTTTAAAAATA
42957470 TTATTAT-TATATTTTTAAAAATA
1 -T-TTATGTATATTTTTAAAAATA
42957493 TTTATGTAT-TTTTTA
1 TTTATGTATATTTTTA
42957508 TTTTTTAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 14 0.42
22 18 0.55
23 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTATGTATATTTTTAAAAATA
Found at i:42957506 original size:22 final size:20
Alignment explanation
Indices: 42957448--42957507 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 20
42957438 AATATTTTTT
42957448 ATTTTATATATTTTTTAAAAA
1 ATTTTAT-TATTTTTTAAAAA
42957469 ATTATTATTATATTTTT-AAAA
1 ATT-TTATTAT-TTTTTAAAAA
42957490 ATATTTATGTATTTTTTA
1 AT-TTTAT-TATTTTTTA
42957508 TTTTTTAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTATTATTTTTTAAAAA
Found at i:42957742 original size:31 final size:32
Alignment explanation
Indices: 42957649--42957742 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 32
42957639 CAATTAACAG
* * * *
42957649 AAATGGAAAAAAGAATCGATTAGTTGGGTGATC
1 AAATGAAAAAAAAAATCCA-TAGTTGGGTGACC
* * *
42957682 AAATTAAAAAAAAAATTCATAATTGGGTGACC
1 AAATGAAAAAAAAAATCCATAGTTGGGTGACC
* *
42957714 AAA-GAAGAAACAAATCCATAGTTGGGTGA
1 AAATGAAAAAAAAAATCCATAGTTGGGTGA
42957743 TCAATTTTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
31 21 0.43
32 14 0.29
33 14 0.29
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (32 bp):
AAATGAAAAAAAAAATCCATAGTTGGGTGACC
Found at i:42966424 original size:17 final size:16
Alignment explanation
Indices: 42966388--42966436 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
42966378 TGATAAATAC
42966388 AAATTTAAAAATAAAA
1 AAATTTAAAAATAAAA
* *
42966404 AAATCTTAAAAATATAT
1 AAAT-TTAAAAATAAAA
42966421 AAA-TTAATAAATAAAA
1 AAATTTAA-AAATAAAA
42966437 GTATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTTAAAAATAAAA
Found at i:42966749 original size:15 final size:14
Alignment explanation
Indices: 42966729--42966758 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
42966719 GTTTTTTTTT
42966729 TATATATTTATATAA
1 TATATATTT-TATAA
42966744 TATATATTTTATAA
1 TATATATTTTATAA
42966758 T
1 T
42966759 TTTTTATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATATTTTATAA
Found at i:42966815 original size:15 final size:15
Alignment explanation
Indices: 42966797--42966827 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42966787 AATTTAATTT
*
42966797 TTATTAATTTATATA
1 TTATAAATTTATATA
42966812 TTATAAATTTATATA
1 TTATAAATTTATATA
42966827 T
1 T
42966828 ATTTCAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATAAATTTATATA
Found at i:42974340 original size:84 final size:80
Alignment explanation
Indices: 42974163--42974401 Score: 217
Period size: 80 Copynumber: 3.0 Consensus size: 80
42974153 AACCAAAGTC
* * * * *
42974163 TTTACAA-AAAATATTATTATGTGGACTATC--T-ATC-TAAAATCTAAAATAATG-CAATGTCT
1 TTTACAATAAAATA-AATTATGTGGACTATCTTTCAACATACAATATAAAATAATGCCAAGGTCT
*
42974222 TTTATTTAATTA-ATT
65 TTTATTTAATTATTTT
* * * *
42974237 TTTACAATAAAATATATTATGTGAAATATCTATCTTTCAACGTGCAATATAAAATAATGCCATAG
1 TTTACAATAAAATAAATTATGTG---GA-CTATCTTTCAACATACAATATAAAATAATGCCA-AG
*
42974302 GTCTTTTATTTATTTATTTAT
61 GTCTTTTATTTAATTATTT-T
* * *
42974323 TTTACAA-AAAA-AAATTATGTGGACTATCTTTCAACATACAATCTACAATAATGCCACAGGTAT
1 TTTACAATAAAATAAATTATGTGGACTATCTTTCAACATACAATATAAAATAATGCCA-AGGTCT
42974386 TTTATTTAATTATTTT
65 TTTATTTAATTATTTT
42974402 GATTTGATTT
Statistics
Matches: 135, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
74 16 0.12
75 6 0.04
77 1 0.01
78 5 0.04
79 1 0.01
80 49 0.36
81 3 0.02
82 14 0.10
83 2 0.01
84 25 0.19
85 5 0.04
86 8 0.06
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (80 bp):
TTTACAATAAAATAAATTATGTGGACTATCTTTCAACATACAATATAAAATAATGCCAAGGTCTT
TTATTTAATTATTTT
Found at i:42975098 original size:25 final size:23
Alignment explanation
Indices: 42975070--42975115 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
42975060 ACTTTATATT
*
42975070 TTTATTTTTATTTTTAAGAATTTAA
1 TTTATTTAT-TTTTTAA-AATTTAA
42975095 TTTATTTATTTTTTAAAATTT
1 TTTATTTATTTTTTAAAATTT
42975116 TTAAATTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTATTTTTTAAAATTTAA
Found at i:42979848 original size:19 final size:19
Alignment explanation
Indices: 42979824--42979862 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42979814 TGACAGGCGC
42979824 AAATTATT-TTTTTATATTA
1 AAATTATTATTTTTAT-TTA
42979843 AAATTATTATTTTTATTTA
1 AAATTATTATTTTTATTTA
42979862 A
1 A
42979863 TAAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATTATTATTTTTATTTA
Found at i:42979854 original size:22 final size:21
Alignment explanation
Indices: 42979826--42979874 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
42979816 ACAGGCGCAA
*
42979826 ATTATTTTT-TTATATTAAAATT
1 ATTATTTTTATT-TAATAAAA-T
42979848 ATTATTTTTATTTAATAAAAT
1 ATTATTTTTATTTAATAAAAT
42979869 ATTATT
1 ATTATT
42979875 AATCTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATTTTTATTTAATAAAAT
Found at i:42979962 original size:27 final size:27
Alignment explanation
Indices: 42979932--42980056 Score: 142
Period size: 27 Copynumber: 4.6 Consensus size: 27
42979922 CAGGTTGCGG
* * *
42979932 CTATTTGATAGGCGCGACTAGTTAAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
42979959 CTATCTCAGAGGCGCGACTAGTTGAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
42979986 TTATCTGACAGGCGTGACTAGTTGAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
42980013 CTATCTGACAGGAGCGACTAGTTGTGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* * *
42980040 CTAACTCAGAGGCGCGA
1 CTATCTGACAGGCGCGA
42980057 ATGGTGGGGC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (27 bp):
CTATCTGACAGGCGCGACTAGTTGAGC
Found at i:42984539 original size:60 final size:60
Alignment explanation
Indices: 42984475--42984607 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 60
42984465 ATACTAAATT
* * * *
42984475 AAACACAACAATTTATAACTTAACCCTAAATTACTAATAAATAAATTTTAAAATAATTAC
1 AAACACAAAAAATTATAACATAACCCTAAATTACTAACAAATAAATTTTAAAATAATTAC
* * *
42984535 AAACACAAAAAATTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAT
1 AAACACAAAAAATTATAACATAACCCTAAATTACTAACAAATAAATTTTAAAATAATTAC
*
42984595 AAAAAGCAAAAAA
1 AAACA-CAAAAAA
42984608 AAAATACATT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 57 0.89
61 7 0.11
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.29
Consensus pattern (60 bp):
AAACACAAAAAATTATAACATAACCCTAAATTACTAACAAATAAATTTTAAAATAATTAC
Found at i:42984712 original size:16 final size:16
Alignment explanation
Indices: 42984687--42984724 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42984677 TGATACATTA
*
42984687 CTCTTTTTTTTCTTTCT
1 CTCTTCTTTTT-TTTCT
42984704 -TCTTCTTTTTTTTCT
1 CTCTTCTTTTTTTTCT
42984719 CTCTTC
1 CTCTTC
42984725 CGAATGTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
CTCTTCTTTTTTTTCT
Found at i:42984712 original size:19 final size:19
Alignment explanation
Indices: 42984688--42984724 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42984678 GATACATTAC
*
42984688 TCTTTTTTTTCTTTCTTCT
1 TCTTTTTTTTCTCTCTTCT
42984707 TCTTTTTTTTCTCTCTTC
1 TCTTTTTTTTCTCTCTTC
42984725 CGAATGTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTTTTTTCTCTCTTCT
Found at i:42984896 original size:27 final size:27
Alignment explanation
Indices: 42984866--42984922 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
42984856 GCCTACCTAT
*
42984866 CAGGCTCGATTAGTCGCGCCTATTTGA
1 CAGGCTCGATTAGTCGCGCCCATTTGA
*
42984893 CAGGCTCGATTAGTCGTGCCCATTTGA
1 CAGGCTCGATTAGTCGCGCCCATTTGA
42984920 CAG
1 CAG
42984923 ACGCGACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (27 bp):
CAGGCTCGATTAGTCGCGCCCATTTGA
Found at i:42991616 original size:24 final size:24
Alignment explanation
Indices: 42991571--42991618 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
42991561 AATCATTTTA
42991571 ATAAAAAAGAAAACATTTTCTTTAGT
1 ATAAAAAAGAAAACA--TTCTTTAGT
42991597 ATAAAAAAGAAAGACA-TCTTTA
1 ATAAAAAAGAAA-ACATTCTTTA
42991619 AATGTCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
26 12 0.57
27 3 0.14
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (24 bp):
ATAAAAAAGAAAACATTCTTTAGT
Found at i:42997369 original size:20 final size:21
Alignment explanation
Indices: 42997315--42997372 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
42997305 TTAATATTTT
* *
42997315 TAAATCTTTATATAT-TTAGA
1 TAAATCTTTAAAAATATTAGA
42997335 TAAAGTC-TT-AAAATATT-GA
1 TAAA-TCTTTAAAAATATTAGA
42997354 TAAATCTTTAAAAATATTA
1 TAAATCTTTAAAAATATTA
42997373 TTAAATTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
TAAATCTTTAAAAATATTAGA
Found at i:43000678 original size:3 final size:3
Alignment explanation
Indices: 43000670--43000701 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
43000660 TATCAAGAAC
43000670 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43000702 GATAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43001634 original size:22 final size:22
Alignment explanation
Indices: 43001608--43001663 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
43001598 AAATTAAATC
43001608 TCTAAGATTGCAGATCATATCT
1 TCTAAGATTGCAGATCATATCT
43001630 TCTAAGATTGCAGATCATATCT
1 TCTAAGATTGCAGATCATATCT
43001652 TCTAAGATTGCA
1 TCTAAGATTGCA
43001664 TATCTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
TCTAAGATTGCAGATCATATCT
Found at i:43005148 original size:2 final size:2
Alignment explanation
Indices: 43005113--43005137 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43005103 GTACATGTAA
43005113 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 A
43005138 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43009675 original size:3 final size:3
Alignment explanation
Indices: 43009667--43009703 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
43009657 ATTTTCCCCA
*
43009667 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
43009704 TCATGTTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43010725 original size:31 final size:31
Alignment explanation
Indices: 43010690--43010787 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
43010680 GATTCGTCTA
43010690 TGTATGCTTGAAAAATATGAAGTTGGTGGTC
1 TGTATGCTTGAAAAATATGAAGTTGGTGGTC
* *
43010721 TGTA----T-AAAATATATGCAG-TGAGATTCGTC
1 TGTATGCTTGAAAA-ATATGAAGTTG-G--TGGTC
43010750 TATGTATGCTTGAAAAATATGAAGTTGGTGGTC
1 --TGTATGCTTGAAAAATATGAAGTTGGTGGTC
43010783 TGTAT
1 TGTAT
43010788 AAAATTCAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 24
0.65 0.05 0.30
Matches are distributed among these distances:
26 6 0.12
27 9 0.18
29 4 0.08
31 13 0.25
33 4 0.08
35 9 0.18
36 6 0.12
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.37
Consensus pattern (31 bp):
TGTATGCTTGAAAAATATGAAGTTGGTGGTC
Found at i:43010753 original size:62 final size:62
Alignment explanation
Indices: 43010667--43010792 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
43010657 TCTGATCAAG
43010667 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
1 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
43010729 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
1 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
43010791 AT
1 AT
43010793 TCAGATTTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.36
Consensus pattern (62 bp):
ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
Found at i:43021632 original size:20 final size:19
Alignment explanation
Indices: 43021587--43021656 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
43021577 GAAGAAAAAA
43021587 AAAAAAGAAAATGGGAAAG
1 AAAAAAGAAAATGGGAAAG
43021606 AATAAAAGAAAA-GGGAAA-
1 AA-AAAAGAAAATGGGAAAG
**
43021624 AGGAAA-AAAATGGGAAAG
1 AAAAAAGAAAATGGGAAAG
* *
43021642 TGAAATAGAAAATGG
1 -AAAAAAGAAAATGG
43021657 ACTATGATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.10
17 9 0.22
18 1 0.03
19 10 0.25
20 16 0.40
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (19 bp):
AAAAAAGAAAATGGGAAAG
Found at i:43022600 original size:52 final size:51
Alignment explanation
Indices: 43022522--43022623 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 51
43022512 CTTGTAGTTC
* * *
43022522 ATAAAAGAAAAAATAGTTTGTGGGTCA-GCAGATGCACTAAAGAGTTATAT
1 ATAAAAAAAAAAATAGTTAGTGGGTCAGGCAAATGCACTAAAGAGTTATAT
* *
43022572 ATAAAAAAAAAAATGTAGTTAGTGGGTCAGGGAAATGCACTCAAGAGTTATA
1 ATAAAAAAAAAAA--TAGTTAGTGGGTCAGGCAAATGCACTAAAGAGTTATA
43022624 AAATCTGACT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
50 12 0.27
52 13 0.30
53 19 0.43
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.25
Consensus pattern (51 bp):
ATAAAAAAAAAAATAGTTAGTGGGTCAGGCAAATGCACTAAAGAGTTATAT
Found at i:43023065 original size:18 final size:19
Alignment explanation
Indices: 43023042--43023086 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
43023032 TATTTTATAT
*
43023042 AATATTTTTA-ATTTTTTA
1 AATATTTTTATAATTTTTA
43023060 AATATTTTTATAATTTTTA
1 AATATTTTTATAATTTTTA
43023079 AATTATTT
1 AA-TATTT
43023087 GTTGGTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.42
19 9 0.38
20 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATATTTTTATAATTTTTA
Found at i:43023073 original size:20 final size:18
Alignment explanation
Indices: 43023042--43023086 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
43023032 TATTTTATAT
43023042 AATA-TTTTTAATTTTTTA
1 AATATTTTTTAA-TTTTTA
43023060 AATATTTTTATAATTTTTA
1 AATATTTTT-TAATTTTTA
43023079 AATTATTT
1 AA-TATTT
43023087 GTTGGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.17
19 12 0.50
20 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
AATATTTTTTAATTTTTA
Found at i:43042511 original size:29 final size:27
Alignment explanation
Indices: 43042478--43042544 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
43042468 TTTTCCCTGG
* *
43042478 GAAAAAATTAAAATTTAATTCTATAAAAA
1 GAAAAAATGAAAA-TCAATT-TATAAAAA
*
43042507 GAAAAAAAGAAAATCAATTTATAAAAA
1 GAAAAAATGAAAATCAATTTATAAAAA
43042534 GATAAAAATGA
1 GA-AAAAATGA
43042545 GTGATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.30
28 12 0.36
29 11 0.33
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (27 bp):
GAAAAAATGAAAATCAATTTATAAAAA
Found at i:43046434 original size:18 final size:18
Alignment explanation
Indices: 43046413--43046478 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
43046403 AATTATTATT
*
43046413 TTTTAAATATTTTTTATA
1 TTTTAAATATTTTTTAAA
*
43046431 TTTTTAATATTTTTTTAAA
1 TTTTAAATA-TTTTTTAAA
* *
43046450 GTTT-AATTTTTTTTAAA
1 TTTTAAATATTTTTTAAA
*
43046467 TTTTAAAAATTT
1 TTTTAAATATTT
43046479 AAAAATTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 12 0.31
18 16 0.41
19 11 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTAAATATTTTTTAAA
Found at i:43046448 original size:11 final size:10
Alignment explanation
Indices: 43046409--43046445 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
43046399 AATTAATTAT
43046409 TATTTTTTAAA
1 TATTTTTT-AA
43046420 TATTTTTT-A
1 TATTTTTTAA
43046429 TA-TTTTTAA
1 TATTTTTTAA
43046438 TATTTTTT
1 TATTTTTT
43046446 TAAAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.21
9 6 0.25
10 5 0.21
11 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:43046460 original size:17 final size:18
Alignment explanation
Indices: 43046433--43046472 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
43046423 TTTTTATATT
43046433 TTTAATATTTTTTTAAAG
1 TTTAATATTTTTTTAAAG
*
43046451 TTTAAT-TTTTTTTAAAT
1 TTTAATATTTTTTTAAAG
43046468 TTTAA
1 TTTAA
43046473 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTAATATTTTTTTAAAG
Found at i:43047577 original size:26 final size:24
Alignment explanation
Indices: 43047531--43047579 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
43047521 AACTTATGAC
43047531 TATATATACAAATTAATTTAATAA
1 TATATATACAAATTAATTTAATAA
*
43047555 TATATTATATAAATATAATTTAATA
1 TATA-TATACAAAT-TAATTTAATA
43047580 TACTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 8 0.36
26 10 0.45
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATATACAAATTAATTTAATAA
Found at i:43047867 original size:14 final size:15
Alignment explanation
Indices: 43047837--43047867 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43047827 ATATAAACAA
43047837 TTTTGAAAATTATTT
1 TTTTGAAAATTATTT
43047852 TTTTGAAAATTATTT
1 TTTTGAAAATTATTT
43047867 T
1 T
43047868 AACATATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTGAAAATTATTT
Found at i:43079322 original size:50 final size:50
Alignment explanation
Indices: 43079245--43079487 Score: 369
Period size: 50 Copynumber: 4.8 Consensus size: 50
43079235 ATTTGGGTAA
43079245 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
43079295 ATAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
43079345 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
43079395 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
43079445 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
43079488 TGTTATTATC
Statistics
Matches: 172, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 138 0.80
51 34 0.20
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:43087202 original size:22 final size:24
Alignment explanation
Indices: 43087154--43087263 Score: 125
Period size: 25 Copynumber: 4.5 Consensus size: 24
43087144 TATACGGAAC
* * *
43087154 AAATACAGAGAGCACAAATGTG-TT
1 AAAT-CAGAGAGCACCAACGTGCTA
**
43087178 AAA-CAGAGAGCACTGACGTGCTA
1 AAATCAGAGAGCACCAACGTGCTA
43087201 AATATCAGAGAGCACCAACGTGCTA
1 AA-ATCAGAGAGCACCAACGTGCTA
43087226 ATAATCAGAGAGCACCAACGTGCTA
1 A-AATCAGAGAGCACCAACGTGCTA
43087251 ATAATCAGAGAGC
1 A-AATCAGAGAGC
43087264 GCGCTAAAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
22 14 0.18
23 3 0.04
24 4 0.05
25 54 0.71
26 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (24 bp):
AAATCAGAGAGCACCAACGTGCTA
Found at i:43087212 original size:25 final size:25
Alignment explanation
Indices: 43087181--43087263 Score: 132
Period size: 25 Copynumber: 3.3 Consensus size: 25
43087171 ATGTGTTAAA
**
43087181 CAGAGAGCACTGACGTGCTAA-ATAT
1 CAGAGAGCACCAACGTGCTAATA-AT
43087206 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
43087231 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
43087256 CAGAGAGC
1 CAGAGAGC
43087264 GCGCTAAAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:43088304 original size:11 final size:11
Alignment explanation
Indices: 43088288--43088313 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43088278 TCTTTCTTTC
43088288 TTTCTCCCCTG
1 TTTCTCCCCTG
43088299 TTTCTCCCCTG
1 TTTCTCCCCTG
43088310 TTTC
1 TTTC
43088314 GTTTCGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:43088387 original size:5 final size:5
Alignment explanation
Indices: 43088369--43088408 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
43088359 TGTTTTATGT
*
43088369 ATATA ATAATA ATATA ATATT ATAATA ATATA ATATA ATA
1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATA
43088409 ACTTACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.71
6 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:43088393 original size:16 final size:16
Alignment explanation
Indices: 43088369--43088409 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
43088359 TGTTTTATGT
43088369 ATATAATAATAATATA
1 ATATAATAATAATATA
*
43088385 ATATTATAATAATATA
1 ATATAATAATAATATA
43088401 ATATAATAA
1 ATATAATAA
43088410 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:43088409 original size:8 final size:8
Alignment explanation
Indices: 43088374--43088403 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
43088364 TATGTATATA
43088374 ATAATAAT
1 ATAATAAT
*
43088382 ATAATATT
1 ATAATAAT
43088390 ATAATAAT
1 ATAATAAT
43088398 ATAATA
1 ATAATA
43088404 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:43093229 original size:52 final size:52
Alignment explanation
Indices: 43093151--43093356 Score: 300
Period size: 52 Copynumber: 4.1 Consensus size: 52
43093141 NNNNNNNNNN
*
43093151 CAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGTAACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
*
43093203 CAAGTAACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTAACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
43093255 CAAG-AGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGTA-ACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
* * **
43093301 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTAACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
43093353 CAAG
1 CAAG
43093357 AGACAAAGTG
Statistics
Matches: 140, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
46 43 0.31
51 1 0.01
52 96 0.69
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (52 bp):
CAAGTAACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
Found at i:43093284 original size:46 final size:46
Alignment explanation
Indices: 43093217--43093373 Score: 224
Period size: 46 Copynumber: 3.3 Consensus size: 46
43093207 TAACAAGTGG
*
43093217 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
*
43093263 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
**
43093309 AAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
43093361 AAAGTGATAAGTG
1 AAAGTGATAAGTG
43093374 GCTACACCTA
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
46 57 0.57
52 43 0.43
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
Found at i:43093334 original size:98 final size:98
Alignment explanation
Indices: 43093165--43093373 Score: 373
Period size: 98 Copynumber: 2.1 Consensus size: 98
43093155 TGACAAGTGG
*
43093165 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTAACAAGTGGAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTAACAAGTGAAAAGTGATAAGTG
* *
43093230 ATAGCTTCGGCTATACTTATCTGATCAAGAGAC
66 ATAGCTTCAGCTACACTTATCTGATCAAGAGAC
*
43093263 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTAACAAGTGAAAAGTGATAAGTG
*
43093328 ATAGCTTTAGCTACACTTATCTGATCAAGAGAC
66 ATAGCTTCAGCTACACTTATCTGATCAAGAGAC
43093361 AAAGTGATAAGTG
1 AAAGTGATAAGTG
43093374 GCTACACCTA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 106 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (98 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTAACAAGTGAAAAGTGATAAGTG
ATAGCTTCAGCTACACTTATCTGATCAAGAGAC
Found at i:43093362 original size:52 final size:53
Alignment explanation
Indices: 43093263--43093373 Score: 179
Period size: 52 Copynumber: 2.1 Consensus size: 53
43093253 ATCAAGAGAC
* *
43093263 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTGA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
*
43093315 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
*
43093368 TAAGTG
1 AAAGTG
43093374 GCTACACCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
52 43 0.80
53 11 0.20
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (53 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
Found at i:43093386 original size:37 final size:37
Alignment explanation
Indices: 43093337--43093445 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
43093327 GATAGCTTTA
43093337 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
43093374 GCTACACCTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
43093411 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
43093446 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 12 0.18
36 4 0.06
37 51 0.76
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:43094445 original size:49 final size:50
Alignment explanation
Indices: 43094375--43094471 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 50
43094365 ACATGTGAAC
* *
43094375 ATGTGATTATGTGATTCCGTGTAAGACCATACCTGGGCTATGGCATCGGT
1 ATGTGATTATGTGATTACGTGTAAGACCATACCTGGACTATGGCATCGGT
**
43094425 ATGTGATT-TGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 ATGTGATTATGTGATTACGTGTAAGACCATACCTGGACTATGGCATCG
43094472 AGAAAACGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 35 0.81
50 8 0.19
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (50 bp):
ATGTGATTATGTGATTACGTGTAAGACCATACCTGGACTATGGCATCGGT
Found at i:43100602 original size:19 final size:19
Alignment explanation
Indices: 43100580--43100616 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
43100570 TTAAGTTTGA
43100580 AAATTTATAAGATTATATT
1 AAATTTATAAGATTATATT
43100599 AAATTTATAAGATTATAT
1 AAATTTATAAGATTATAT
43100617 ACAAAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTATAAGATTATATT
Found at i:43119059 original size:29 final size:29
Alignment explanation
Indices: 43119016--43119077 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
43119006 TTATAATAAG
* *
43119016 TCATATTATTCTAAGATATTTTAGTCTTT
1 TCATACTATTCTAAGATATTTTAGTCTCT
* * *
43119045 TCATACTATTTTAAGTTTTTTTAGTCTCT
1 TCATACTATTCTAAGATATTTTAGTCTCT
43119074 TCAT
1 TCAT
43119078 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.56
Consensus pattern (29 bp):
TCATACTATTCTAAGATATTTTAGTCTCT
Found at i:43119557 original size:3 final size:3
Alignment explanation
Indices: 43119549--43119575 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43119539 TGTGGATTAA
43119549 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
43119576 TTGGTATAAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43127677 original size:29 final size:30
Alignment explanation
Indices: 43127614--43127695 Score: 112
Period size: 29 Copynumber: 2.7 Consensus size: 30
43127604 ATTCTGAAAA
*
43127614 TTATATATAAATTTTAATTTAATGTACAATG
1 TTATATATAAATTTTAATTTTATG-ACAATG
* *
43127645 TTATACATAAATTTTAATTTTATG-CAATT
1 TTATATATAAATTTTAATTTTATGACAATG
*
43127674 TTATATATGAATTTTAATTTTA
1 TTATATATAAATTTTAATTTTA
43127696 CACATGAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.52
31 22 0.48
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATATATAAATTTTAATTTTATGACAATG
Found at i:43127694 original size:19 final size:19
Alignment explanation
Indices: 43127670--43127707 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43127660 AATTTTATGC
* *
43127670 AATTTTATATATGAATTTT
1 AATTTTACACATGAATTTT
43127689 AATTTTACACATGAATTTT
1 AATTTTACACATGAATTTT
43127708 TTATTTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
AATTTTACACATGAATTTT
Found at i:43133673 original size:36 final size:36
Alignment explanation
Indices: 43133621--43133692 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
43133611 GATGAGCTTA
43133621 TGTAGTTTACTACTTCCATGCTCACAGACTAGTTTT
1 TGTAGTTTACTACTTCCATGCTCACAGACTAGTTTT
*
43133657 TGTAGTTTACTGCTTCCATGCTCACAGACTAGTTTT
1 TGTAGTTTACTACTTCCATGCTCACAGACTAGTTTT
43133693 CTTTCCCTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (36 bp):
TGTAGTTTACTACTTCCATGCTCACAGACTAGTTTT
Found at i:43143245 original size:6 final size:6
Alignment explanation
Indices: 43143236--43143274 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
43143226 TCCTGACACT
43143236 TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCT
1 TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCT
43143275 TTCATGCGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTATC
Found at i:43144435 original size:25 final size:26
Alignment explanation
Indices: 43144378--43144435 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
43144368 TATTTATCAT
*
43144378 ATAA-TTATTATATTATTTTAAGATA
1 ATAATTTATTATATTAATTTAAGATA
43144403 A-AATTTTATTA-ATTAATTTAATG-TA
1 ATAA-TTTATTATATTAATTTAA-GATA
43144428 ATAATTTA
1 ATAATTTA
43144436 AAGAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 2 0.07
25 17 0.61
26 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
ATAATTTATTATATTAATTTAAGATA
Found at i:43153898 original size:4 final size:4
Alignment explanation
Indices: 43153884--43153912 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
43153874 GGAGTGAATG
43153884 GAAA G-AA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
43153913 GTTGGTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:43167929 original size:19 final size:19
Alignment explanation
Indices: 43167907--43167953 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
43167897 AATATAATAT
43167907 AATTATATAA-TTATATCAA
1 AATTATATAATTTATAT-AA
*
43167926 AATTGA-ATAATTTATATAT
1 AATT-ATATAATTTATATAA
43167945 AATTATATA
1 AATTATATA
43167954 GATATTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 16 0.67
20 7 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTATATAATTTATATAA
Found at i:43168259 original size:17 final size:18
Alignment explanation
Indices: 43168231--43168264 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
43168221 AAAAATATAA
43168231 GAAAACATATAAAATTAT
1 GAAAACATATAAAATTAT
43168249 GAAAA-ATATAAAATTA
1 GAAAACATATAAAATTA
43168265 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
GAAAACATATAAAATTAT
Found at i:43170500 original size:31 final size:31
Alignment explanation
Indices: 43170465--43170528 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
43170455 CAGCCTAGTA
* *
43170465 ACTTAAATAAAAATTTTTAAATAGTTCAATG
1 ACTTAAATAAAAACTTTCAAATAGTTCAATG
* * *
43170496 ACTTAAATGAAAACTTTCGAATAGTTCAGTG
1 ACTTAAATAAAAACTTTCAAATAGTTCAATG
43170527 AC
1 AC
43170529 CAAATTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGTTCAATG
Found at i:43191937 original size:21 final size:21
Alignment explanation
Indices: 43191900--43191941 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
43191890 ATCATAAATT
43191900 TGTTTATTATTATATTTTTTA
1 TGTTTATTATTATATTTTTTA
* *
43191921 TGTTT-TTTTTATAATTTTTA
1 TGTTTATTATTATATTTTTTA
43191941 T
1 T
43191942 AATTTTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (21 bp):
TGTTTATTATTATATTTTTTA
Found at i:43191947 original size:20 final size:20
Alignment explanation
Indices: 43191909--43191948 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43191899 TTGTTTATTA
* **
43191909 TTATATTTTTTATGTTTTTT
1 TTATAATTTTTATAATTTTT
43191929 TTATAATTTTTATAATTTTT
1 TTATAATTTTTATAATTTTT
43191949 AGAAGATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
TTATAATTTTTATAATTTTT
Found at i:43203920 original size:1 final size:1
Alignment explanation
Indices: 43203888--43203912 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43203878 AACAATGACC
43203888 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
43203913 CTGTTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43206269 original size:18 final size:18
Alignment explanation
Indices: 43206246--43206281 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43206236 TTATTATTTT
43206246 TAAAATTATAAAAATATA
1 TAAAATTATAAAAATATA
*
43206264 TAAAATTATTAAAATATA
1 TAAAATTATAAAAATATA
43206282 CACATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATTATAAAAATATA
Found at i:43208880 original size:5 final size:5
Alignment explanation
Indices: 43208872--43208897 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43208862 TACAGTCTCG
43208872 TCTTC TCTTC TCTTC TCTTC TCTTC T
1 TCTTC TCTTC TCTTC TCTTC TCTTC T
43208898 TACAGCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCTTC
Found at i:43212017 original size:14 final size:14
Alignment explanation
Indices: 43211998--43212035 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
43211988 TTTGCTCGAG
43211998 ATGAAATATCAAAC
1 ATGAAATATCAAAC
*
43212012 ATGAAATACCAAAC
1 ATGAAATATCAAAC
43212026 ATGAAATATC
1 ATGAAATATC
43212036 CATTTGCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.21
Consensus pattern (14 bp):
ATGAAATATCAAAC
Found at i:43212032 original size:50 final size:50
Alignment explanation
Indices: 43211973--43212069 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
43211963 CTTAACTCTT
43211973 AACATGAAATATCCATTTGCTCGAGATGAAATATCAAACATGAAATACCA
1 AACATGAAATATCCATTTGCTCGAGATGAAATATCAAACATGAAATACCA
*
43212023 AACATGAAATATCCATTTGCTCGATATGAAATATCAAACATGAAATA
1 AACATGAAATATCCATTTGCTCGAGATGAAATATCAAACATGAAATA
43212070 TCCATTTGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (50 bp):
AACATGAAATATCCATTTGCTCGAGATGAAATATCAAACATGAAATACCA
Found at i:43212052 original size:36 final size:36
Alignment explanation
Indices: 43212012--43212088 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
43212002 AATATCAAAC
*
43212012 ATGAAATACCAAACATGAAATATCCATTTGCTCGAT
1 ATGAAATACCAAACATGAAATATCCATTTGCTCGAG
*
43212048 ATGAAATATCAAACATGAAATATCCATTTGCTCGAG
1 ATGAAATACCAAACATGAAATATCCATTTGCTCGAG
43212084 ATGAA
1 ATGAA
43212089 TGGTAAGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (36 bp):
ATGAAATACCAAACATGAAATATCCATTTGCTCGAG
Found at i:43214569 original size:18 final size:20
Alignment explanation
Indices: 43214543--43214579 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
43214533 ACAAAGGAAA
*
43214543 AGAATGAAACAGAG-ATTAG
1 AGAATGAAAAAGAGCATTAG
43214562 AGAA-GAAAAAGAGCATTA
1 AGAATGAAAAAGAGCATTA
43214580 CAGGCCAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (20 bp):
AGAATGAAAAAGAGCATTAG
Found at i:43220044 original size:23 final size:23
Alignment explanation
Indices: 43220018--43220061 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
43220008 ATCACCTAAC
*
43220018 ATTAATGGTGTTATGAAAATTTG
1 ATTAATGATGTTATGAAAATTTG
43220041 ATTAATGATGTTATGAAAATT
1 ATTAATGATGTTATGAAAATT
43220062 ACGTGACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGATGTTATGAAAATTTG
Found at i:43220795 original size:10 final size:10
Alignment explanation
Indices: 43220782--43220812 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
43220772 AGTTAAAGAC
43220782 CTTTTTAGTG
1 CTTTTTAGTG
43220792 CTTTTTAGTG
1 CTTTTTAGTG
*
43220802 TTTTTTAGTG
1 CTTTTTAGTG
43220812 C
1 C
43220813 ATATTATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.61
Consensus pattern (10 bp):
CTTTTTAGTG
Found at i:43221349 original size:3 final size:3
Alignment explanation
Indices: 43221341--43221370 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43221331 CTAGTACAAA
43221341 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
43221371 AAAAGGGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:43223510 original size:15 final size:15
Alignment explanation
Indices: 43223490--43223534 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
43223480 CATTTGGTAC
43223490 TTTAATTTGACATTT
1 TTTAATTTGACATTT
*
43223505 TTTAATTT-A-ATAT
1 TTTAATTTGACATTT
*
43223518 TTAAATTTGAC-TTT
1 TTTAATTTGACATTT
43223532 TTT
1 TTT
43223535 TTCCTAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
13 10 0.42
14 6 0.25
15 8 0.33
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (15 bp):
TTTAATTTGACATTT
Found at i:43229752 original size:13 final size:13
Alignment explanation
Indices: 43229734--43229758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43229724 GTTCTTGTGT
43229734 TTTTCTTATTTTA
1 TTTTCTTATTTTA
43229747 TTTTCTTATTTT
1 TTTTCTTATTTT
43229759 TTTGTGTTTG
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTATTTTA
Found at i:43231007 original size:28 final size:26
Alignment explanation
Indices: 43230973--43231030 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
43230963 TCTTATTATA
* *
43230973 TATATCTTTATCTACATATATATATTTT
1 TATATC-TTAT-TACATATATACATCTT
*
43231001 TATATCTTATTATATATATACATCTT
1 TATATCTTATTACATATATACATCTT
43231027 TATA
1 TATA
43231031 CACGTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 17 0.63
27 4 0.15
28 6 0.22
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
TATATCTTATTACATATATACATCTT
Found at i:43231014 original size:20 final size:21
Alignment explanation
Indices: 43230948--43231019 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
43230938 TTCATACATA
*
43230948 TATATATATTTTAGATCTTAT
1 TATATATATTTTATATCTTAT
* *
43230969 TATATATATCTT-TATC-TACA
1 TATATATATTTTATATCTTA-T
43230989 TATATATATTTTTATATCTTAT
1 TATATATA-TTTTATATCTTAT
43231011 TATATATAT
1 TATATATAT
43231020 ACATCTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 2 0.05
20 11 0.26
21 15 0.36
22 12 0.29
23 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (21 bp):
TATATATATTTTATATCTTAT
Found at i:43237228 original size:139 final size:140
Alignment explanation
Indices: 43236965--43237302 Score: 371
Period size: 139 Copynumber: 2.4 Consensus size: 140
43236955 GGTAACAAAA
* * * * *
43236965 GGGAGCAGACTAAAGCCACTAATCATATTTCCCTGAAGTTGCAGTGAAGCGGATTAAAACGAGGA
1 GGGAGCAGACTAAAGCTACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACAAGGA
* * * **
43237030 ATCCTATACCTTTGAAGTTGCAAAGGGTCAGATTAAATTTTATCATAACAAGTCGTATCTCCCTG
66 ATCATATACCTCTGAAGTTGCAAAGGGTCAGATTAAATCTTATCATAACAAACCGTATCTCCCTG
* *
43237095 AAGTTGCAGT
131 AAATCGCAGT
*
43237105 GGGA-CAGACTAAAGCTACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACAATGA
1 GGGAGCAGACTAAAGCTACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACAAGGA
* * * * *
43237169 ATCATATACCTCTGAAGTTGCAGTA-GGTC-GAATTAGATCTTATCATATCAAACCTTATCTCCT
66 ATCATATACCTCTGAAGTTGCA-AAGGGTCAG-ATTAAATCTTATCATAACAAACCGTATCTCCC
43237232 TGAAATCGCAGT
129 TGAAATCGCAGT
** ** * * * * *
43237244 -TTAGCAGGTTGAAGATAC-AAGTCTTATCTCCCTGACGTTGCAGTGGAGCAGACTAAAAC
1 GGGAGCAGACTAAAGCTACTAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC
43237303 CACAAACTTC
Statistics
Matches: 167, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
138 4 0.02
139 158 0.95
140 5 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (140 bp):
GGGAGCAGACTAAAGCTACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACAAGGA
ATCATATACCTCTGAAGTTGCAAAGGGTCAGATTAAATCTTATCATAACAAACCGTATCTCCCTG
AAATCGCAGT
Found at i:43237989 original size:13 final size:13
Alignment explanation
Indices: 43237971--43237995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43237961 GTTCTTGTGT
43237971 TTTTCTTATTTTA
1 TTTTCTTATTTTA
43237984 TTTTCTTATTTT
1 TTTTCTTATTTT
43237996 TTTGTGTTTG
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTATTTTA
Found at i:43239346 original size:2 final size:2
Alignment explanation
Indices: 43239339--43239389 Score: 68
Period size: 2 Copynumber: 25.5 Consensus size: 2
43239329 CTACGATTTT
* *
43239339 TA TA TA TA TT TA TA TA CA TA T- TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
43239381 TA TA TA TA T
1 TA TA TA TA T
43239390 CTTTACTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43240609 original size:9 final size:9
Alignment explanation
Indices: 43240595--43240738 Score: 66
Period size: 9 Copynumber: 15.4 Consensus size: 9
43240585 GACATGTGGC
43240595 AAAAATTAT
1 AAAAATTAT
43240604 AAAAA-T-T
1 AAAAATTAT
*
43240611 AAATATTAAT
1 AAAAATT-AT
*
43240621 AAAAGTTAT
1 AAAAATTAT
43240630 AAAAA-TATT
1 AAAAATTA-T
*
43240639 AAATATTAAT
1 AAAAATT-AT
*
43240649 AAAAAATTTT
1 -AAAAATTAT
43240659 AAAAA-TAT
1 AAAAATTAT
* *
43240667 TAAAATTAGAAA
1 AAAAATT---AT
43240679 AAAAATT-T
1 AAAAATTAT
*
43240687 AAAAATCAT
1 AAAAATTAT
43240696 AAAAATT-T
1 AAAAATTAT
43240704 ATAAAATATAT
1 A-AAAAT-TAT
* *
43240715 AGAAATATAGA
1 AAAAAT-TA-T
43240726 AAAAATTAT
1 AAAAATTAT
43240735 AAAA
1 AAAA
43240739 TTTTATAAAG
Statistics
Matches: 101, Mismatches: 18, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
7 5 0.05
8 18 0.18
9 38 0.38
10 19 0.19
11 14 0.14
12 7 0.07
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:43240663 original size:29 final size:29
Alignment explanation
Indices: 43240595--43240722 Score: 126
Period size: 28 Copynumber: 4.6 Consensus size: 29
43240585 GACATGTGGC
43240595 AAAAATTAT-AAAA-ATTAAATATTAAT-
1 AAAAATTATAAAAATATTAAATATTAATA
*
43240621 AAAAGTTATAAAAATATTAAATATTAATA
1 AAAAATTATAAAAATATTAAATATTAATA
* *
43240650 AAAAATTTTAAAAATATTAAA-ATTAGAAA
1 AAAAATTATAAAAATATTAAATATTA-ATA
* *
43240679 AAAAATT-TAAAAATCA-TAAAAATTTATA
1 AAAAATTATAAAAAT-ATTAAATATTAATA
* *
43240707 AAATA-TATAGAAATAT
1 AAAAATTATAAAAATAT
43240723 AGAAAAAATT
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.09
27 6 0.07
28 40 0.47
29 32 0.37
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTATAAAAATATTAAATATTAATA
Found at i:43240707 original size:10 final size:10
Alignment explanation
Indices: 43240621--43240747 Score: 52
Period size: 10 Copynumber: 13.2 Consensus size: 10
43240611 AAATATTAAT
*
43240621 AAAAGTTATA
1 AAAATTTATA
*
43240631 AAAATAT-TA
1 AAAATTTATA
* *
43240640 AATATTAATAA
1 AAAATTTAT-A
43240651 AAAATTT-TA
1 AAAATTTATA
*
43240660 AAAA--TATT
1 AAAATTTATA
* *
43240668 AAAATTAGAAA
1 AAAATT-TATA
*
43240679 AAAAATT-TA
1 AAAATTTATA
*
43240688 AAAA-TCATA
1 AAAATTTATA
43240697 AAAATTTAT-
1 AAAATTTATA
*
43240706 AAAATATATA
1 AAAATTTATA
* * *
43240716 GAAATATAGA
1 AAAATTTATA
*
43240726 AAAAATTATA
1 AAAATTTATA
*
43240736 AAATTTTATA
1 AAAATTTATA
43240746 AA
1 AA
43240748 GTCGTAAGAA
Statistics
Matches: 83, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
7 1 0.01
8 6 0.07
9 30 0.36
10 34 0.41
11 12 0.14
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAATTTATA
Found at i:43240758 original size:39 final size:40
Alignment explanation
Indices: 43240687--43240771 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 40
43240677 AAAAAAATTT
43240687 AAAAATCATAAAAATTTATAAAATATATAG-AAA-TATAGA
1 AAAAATCATAAAAATTTATAAAATATATAGAAAATTATA-A
* * * *
43240726 AAAAATTATAAAATTTTATAAAGTCGTA-AGAAAATTATAA
1 AAAAATCATAAAAATTTATAAAAT-ATATAGAAAATTATAA
43240766 AAAAAT
1 AAAAAT
43240772 GTAAAGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
39 23 0.59
40 12 0.31
41 4 0.10
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (40 bp):
AAAAATCATAAAAATTTATAAAATATATAGAAAATTATAA
Found at i:43241084 original size:10 final size:9
Alignment explanation
Indices: 43241068--43241131 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 9
43241058 ATTTTTTCTA
43241068 ATTTTTAAT
1 ATTTTTAAT
43241077 ATTCTTTAAT
1 ATT-TTTAAT
*
43241087 ATTTTTATT
1 ATTTTTAAT
*
43241096 AATATTTAAT
1 -ATTTTTAAT
*
43241106 CATTTTTATAA
1 -ATTTTTA-AT
43241117 ATTTTT-AT
1 ATTTTTAAT
43241125 ATTTTTA
1 ATTTTTA
43241132 TAATTTTACA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
8 7 0.16
9 8 0.18
10 28 0.64
11 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:43241088 original size:29 final size:30
Alignment explanation
Indices: 43241055--43241124 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
43241045 TTACAATATT
*
43241055 TATATTTTT-TCTAATTTTTAAT-ATTCTTTA
1 TATATTTTTAT-TAATATTTAATCATT-TTTA
43241085 -ATATTTTTATTAATATTTAATCATTTTTA
1 TATATTTTTATTAATATTTAATCATTTTTA
*
43241114 TAAATTTTTAT
1 TATATTTTTAT
43241125 ATTTTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (30 bp):
TATATTTTTATTAATATTTAATCATTTTTA
Found at i:43241090 original size:19 final size:18
Alignment explanation
Indices: 43241068--43241131 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
43241058 ATTTTTTCTA
43241068 ATTTTTAATATTCTTTAAT
1 ATTTTTAATATT-TTTAAT
* *
43241087 ATTTTTATTAATATTTAAT
1 ATTTTTAAT-ATTTTTAAT
*
43241106 CATTTTTATAAATTTTT-AT
1 -ATTTTTA-ATATTTTTAAT
43241125 ATTTTTA
1 ATTTTTA
43241132 TAATTTTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 7 0.19
19 16 0.43
20 14 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAATATTTTTAAT
Found at i:43241128 original size:18 final size:17
Alignment explanation
Indices: 43241081--43241139 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 17
43241071 TTTAATATTC
43241081 TTTAATATTTTTATTAAT
1 TTTAATATTTTTA-TAAT
43241099 ATTTAATCATTTTTATAAAT
1 -TTTAAT-ATTTTTAT-AAT
*
43241119 TTTTATATTTTTATAAT
1 TTTAATATTTTTATAAT
43241136 TTTA
1 TTTA
43241140 CAAAATTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 6 0.17
18 8 0.22
19 12 0.33
20 10 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATATTTTTATAAT
Found at i:43241137 original size:9 final size:9
Alignment explanation
Indices: 43241002--43241138 Score: 73
Period size: 9 Copynumber: 14.4 Consensus size: 9
43240992 TTTCATAATT
*
43241002 TTTTTATAC
1 TTTTTATAA
43241011 TTTTTATAAAA
1 TTTTTAT--AA
*
43241022 TTTTATAAAA
1 TTTT-TATAA
* *
43241032 TTTTTTTTAT
1 -TTTTTATAA
*
43241042 TTTTTACAA
1 TTTTTATAA
* *
43241051 TATTTATAT
1 TTTTTATAA
*
43241060 TTTTTCTAA
1 TTTTTATAA
43241069 TTTTTA-ATA
1 TTTTTATA-A
43241078 TTCTTTA-ATA
1 TT-TTTATA-A
43241088 TTTTTATTAA
1 TTTTTA-TAA
* *
43241098 TATTTAATCA
1 T-TTTTATAA
43241108 TTTTTATAAA
1 TTTTTAT-AA
43241118 TTTTTAT-A
1 TTTTTATAA
43241126 TTTTTATAA
1 TTTTTATAA
43241135 TTTT
1 TTTT
43241139 ACAAAATTAG
Statistics
Matches: 98, Mismatches: 19, Indels: 22
0.71 0.14 0.16
Matches are distributed among these distances:
8 9 0.09
9 47 0.48
10 26 0.27
11 14 0.14
12 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43241978 original size:6 final size:6
Alignment explanation
Indices: 43241964--43242082 Score: 123
Period size: 6 Copynumber: 19.8 Consensus size: 6
43241954 CCGGCTTCGA
* *
43241964 CTCCGG CTCCTG CTCGTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
* * * * * *
43242012 CTCCTG CTCCTG CACCTG CAT-CTG CACCTG CTCCTA CTCGTG CTGCTA
1 CTCCTG CTCCTG CTCCTG C-TCCTG CTCCTG CTCCTG CTCCTG CTCCTG
* * *
43242060 CTCCTA CTCCTA CTCCTA CTCCT
1 CTCCTG CTCCTG CTCCTG CTCCT
43242083 ACTACCGCTT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
6 97 1.00
ACGTcount: A:0.07, C:0.47, G:0.15, T:0.31
Consensus pattern (6 bp):
CTCCTG
Found at i:43245767 original size:27 final size:29
Alignment explanation
Indices: 43245710--43245781 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 29
43245700 ACTCATTAAT
*
43245710 ATTATAAATATTATTAACAAGATGTAAAA
1 ATTATAAATATTATTAACAAGATATAAAA
*
43245739 ATTATAAATGATTATT-A-AA-ATATACAA
1 ATTATAAAT-ATTATTAACAAGATATAAAA
*
43245766 ATTATAAA-ATAATTAA
1 ATTATAAATATTATTAA
43245782 TAATTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 5 0.13
26 1 0.03
27 14 0.37
28 2 0.05
29 10 0.26
30 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTATAAATATTATTAACAAGATATAAAA
Found at i:43260456 original size:3 final size:3
Alignment explanation
Indices: 43260448--43260472 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43260438 CGAAAAATAT
43260448 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
43260473 GAGTGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43269022 original size:2 final size:2
Alignment explanation
Indices: 43269017--43269042 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43269007 AGAAAAAAAT
43269017 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
43269043 GCTAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43279873 original size:49 final size:49
Alignment explanation
Indices: 43279817--43279917 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
43279807 GCAGATTATG
*
43279817 TGATGTGGTTAACCTTATCATTTATTTTTAAGTTTCCTTGCCAATGAAC
1 TGATGTGGTTAACCGTATCATTTATTTTTAAGTTTCCTTGCCAATGAAC
*
43279866 TGATGTGGTTAACCGTATCATTTATTTTTATGTTTCCTTGCCAATGAAC
1 TGATGTGGTTAACCGTATCATTTATTTTTAAGTTTCCTTGCCAATGAAC
43279915 TGA
1 TGA
43279918 GACATGGTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (49 bp):
TGATGTGGTTAACCGTATCATTTATTTTTAAGTTTCCTTGCCAATGAAC
Found at i:43281551 original size:27 final size:27
Alignment explanation
Indices: 43281513--43281568 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
43281503 ACTATTAGCA
43281513 GTTAGAACTTATATTGCTAGCTCTAGT
1 GTTAGAACTTATATTGCTAGCTCTAGT
43281540 GTTAGAACTTATATTGCTAGCTCTAGT
1 GTTAGAACTTATATTGCTAGCTCTAGT
43281567 GT
1 GT
43281569 ACCAGACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (27 bp):
GTTAGAACTTATATTGCTAGCTCTAGT
Found at i:43287083 original size:15 final size:15
Alignment explanation
Indices: 43287063--43287095 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43287053 AATTGAATTC
43287063 AAATTTTAAAATATA
1 AAATTTTAAAATATA
*
43287078 AAATTTTAAAGTATA
1 AAATTTTAAAATATA
43287093 AAA
1 AAA
43287096 ACTTAGAGAT
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:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AAATTTTAAAATATA
Found at i:43299599 original size:18 final size:18
Alignment explanation
Indices: 43299559--43299600 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43299549 AATATATAAT
*
43299559 ATTAA-TTATTAAGTTCG
1 ATTAATTTATTAAGTTCA
43299576 ATTAATTTAGTTAA-TTCA
1 ATTAATTTA-TTAAGTTCA
43299594 ATTAATT
1 ATTAATT
43299601 ACTCGATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTAATTTATTAAGTTCA
Found at i:43300417 original size:31 final size:32
Alignment explanation
Indices: 43300381--43300445 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
43300371 CTTAGATAAT
43300381 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
*
43300412 TTTAAAGAGTTTTTATTATGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
43300444 TT
1 TT
43300446 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:43300753 original size:3 final size:3
Alignment explanation
Indices: 43300745--43300803 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
43300735 ATCTATCCTT
43300745 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43300793 TTA TTA TTA TT
1 TTA TTA TTA TT
43300804 TAACTATTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43301089 original size:12 final size:12
Alignment explanation
Indices: 43301069--43301099 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43301059 CAAAAAGTGC
*
43301069 AAAAGAACCGCA
1 AAAAAAACCGCA
43301081 AAAAAAACCGCA
1 AAAAAAACCGCA
43301093 AAAAAAA
1 AAAAAAA
43301100 GTTGCCTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.19, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAACCGCA
Found at i:43302778 original size:3 final size:3
Alignment explanation
Indices: 43302770--43302810 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
43302760 AAATATATCC
43302770 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43302811 AACTAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43306386 original size:24 final size:24
Alignment explanation
Indices: 43306359--43306405 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43306349 TTCGAAATTA
*
43306359 AATTATATATTTT-TATAATTTAAT
1 AATT-TATATTTTATAAAATTTAAT
43306383 AATTTATATTTTATAAAATTTAA
1 AATTTATATTTTATAAAATTTAA
43306406 AGAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTTATATTTTATAAAATTTAAT
Found at i:43311092 original size:15 final size:15
Alignment explanation
Indices: 43311072--43311100 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43311062 GGTCCCCTAC
43311072 AAAAATTAAGTCTTG
1 AAAAATTAAGTCTTG
43311087 AAAAATTAAGTCTT
1 AAAAATTAAGTCTT
43311101 AGTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (15 bp):
AAAAATTAAGTCTTG
Found at i:43311226 original size:15 final size:15
Alignment explanation
Indices: 43311206--43311235 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43311196 TATTTAAAGG
*
43311206 ATAAAATTAAAAGAA
1 ATAAAATAAAAAGAA
43311221 ATAAAATAAAAAGAA
1 ATAAAATAAAAAGAA
43311236 GTAGAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
ATAAAATAAAAAGAA
Found at i:43317568 original size:27 final size:27
Alignment explanation
Indices: 43317488--43317569 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
43317478 TTGTATAAAT
*
43317488 TATAAAATTTGTAAAAA-TATTAAAAA
1 TATAAAAATTGTAAAAATTATTAAAAA
* * **
43317514 T-TAAAAATTTTATAAATTACAAAAAA
1 TATAAAAATTGTAAAAATTATTAAAAA
*
43317540 TATGAAAATTGTAAAAATTATTAAAAA
1 TATAAAAATTGTAAAAATTATTAAAAA
43317567 TAT
1 TAT
43317570 TAATGAAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
25 12 0.27
26 9 0.20
27 23 0.52
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (27 bp):
TATAAAAATTGTAAAAATTATTAAAAA
Found at i:43317612 original size:9 final size:9
Alignment explanation
Indices: 43317484--43317616 Score: 69
Period size: 9 Copynumber: 14.4 Consensus size: 9
43317474 AAAGTTGTAT
43317484 AAATTATAA
1 AAATTATAA
* *
43317493 AATTTGTAA
1 AAATTATAA
43317502 AAA-TATTAA
1 AAATTA-TAA
43317511 AAA-T-TAA
1 AAATTATAA
* *
43317518 AAATTTTAT
1 AAATTATAA
*
43317527 AAATTACAA
1 AAATTATAA
* *
43317536 AAAATATGA
1 AAATTATAA
*
43317545 AAATTGTAA
1 AAATTATAA
43317554 AAATTATTAA
1 AAATTA-TAA
43317564 AAA-TATTAA
1 AAATTA-TAA
*
43317573 TGAAATTAACAA
1 --AAATT-ATAA
43317585 AATATTATAA
1 AA-ATTATAA
*
43317595 AACA-CATAA
1 AA-ATTATAA
43317604 AAATTATAA
1 AAATTATAA
43317613 AAAT
1 AAAT
43317617 AAAATAAAAT
Statistics
Matches: 94, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.06
8 3 0.03
9 61 0.65
10 14 0.15
11 6 0.06
12 3 0.03
13 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:43317674 original size:19 final size:20
Alignment explanation
Indices: 43317634--43317674 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43317624 AATAATATGA
*
43317634 AAAAATATAAAACTAACCTT
1 AAAAATATAAAACTAACATT
*
43317654 AAAAATATGAAACT-ACATT
1 AAAAATATAAAACTAACATT
43317673 AA
1 AA
43317675 CATTACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAATATAAAACTAACATT
Found at i:43317992 original size:10 final size:9
Alignment explanation
Indices: 43317951--43318079 Score: 56
Period size: 10 Copynumber: 14.0 Consensus size: 9
43317941 ATTTCTATAT
43317951 TTTTATAATA
1 TTTT-TAATA
43317961 TTTTTAATAA
1 TTTTTAAT-A
43317971 TATTTT-ATA
1 T-TTTTAATA
43317980 TTTTTAAATA
1 TTTTT-AATA
**
43317990 TTTTTCTTAA
1 TTTTTAAT-A
*
43318000 TTTATAAT-
1 TTTTTAATA
*
43318008 TTTTTATTA
1 TTTTTAATA
*
43318017 TGTTCATAAT-
1 T-TT-TTAATA
*
43318027 TTATATAAT-
1 TT-TTTAATA
43318036 TTTTTAATA
1 TTTTTAATA
43318045 -TTTTAATA
1 TTTTTAATA
43318053 TTTTCT-A-A
1 TTTT-TAATA
43318061 TTTTTAATTA
1 TTTTTAA-TA
*
43318071 ATTTTAATA
1 TTTTTAATA
43318080 ACTTTTGACG
Statistics
Matches: 93, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
7 1 0.01
8 29 0.31
9 22 0.24
10 34 0.37
11 7 0.08
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTAATA
Found at i:43317993 original size:68 final size:70
Alignment explanation
Indices: 43317843--43317994 Score: 163
Period size: 69 Copynumber: 2.2 Consensus size: 70
43317833 TTATATGTAA
* * *
43317843 AATTGTAAATATTTTTAATATTTTTTTAAATTTTATATTGTTTTTGAATATTTTGTAATAATATT
1 AATTTTAAATATTTTTAATATTTTTTCAAATTTTATATTGTTTATGAATATTTTGTAATAATATT
*
43317908 TTTGT
66 TTTAT
** * *
43317913 AATTTTCCAT-TTTTATAAT-TTTTTGCACATTTCTATATT-TTTAT-AATATTTT-TAATAATA
1 AATTTTAAATATTTT-TAATATTTTTTCAAATTT-TATATTGTTTATGAATATTTTGTAATAATA
43317973 -TTTTAT
64 TTTTTAT
*
43317979 ATTTTTAAATATTTTT
1 AATTTTAAATATTTTT
43317995 CTTAATTTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
66 13 0.19
67 12 0.18
68 8 0.12
69 18 0.26
70 17 0.25
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (70 bp):
AATTTTAAATATTTTTAATATTTTTTCAAATTTTATATTGTTTATGAATATTTTGTAATAATATT
TTTAT
Found at i:43318012 original size:28 final size:29
Alignment explanation
Indices: 43317941--43318048 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
43317931 TTTTTTGCAC
* *
43317941 ATTTCTAT-ATTTTTATAATATTTTTAATA
1 ATTTATATAATTTTT-TAATATTTTTCATA
* * *
43317970 ATATTTTAT-ATTTTTAAATATTTTTCTTA
1 AT-TTATATAATTTTTTAATATTTTTCATA
* *
43317999 A-TT-TATAATTTTTTATTA-TGTTCATA
1 ATTTATATAATTTTTTAATATTTTTCATA
43318025 ATTTATATAATTTTTTAATATTTT
1 ATTTATATAATTTTTTAATATTTT
43318049 AATATTTTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
26 10 0.16
27 13 0.20
28 14 0.22
29 16 0.25
30 11 0.17
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (29 bp):
ATTTATATAATTTTTTAATATTTTTCATA
Found at i:43318026 original size:26 final size:26
Alignment explanation
Indices: 43317997--43318080 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 26
43317987 ATATTTTTCT
*
43317997 TAATTTATAATTTTTTATTATGTTCA
1 TAATTTATAATTTTTTATTATGTTAA
* *
43318023 TAATTTATATAATTTTTTAATATTTTAA
1 TAA-TT-TATAATTTTTTATTATGTTAA
* * * *
43318051 TATTTTCTAATTTTTAATTAATTTTAA
1 TAATTTATAATTTTTTATT-ATGTTAA
43318078 TAA
1 TAA
43318081 CTTTTGACGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
26 14 0.30
27 13 0.28
28 20 0.43
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (26 bp):
TAATTTATAATTTTTTATTATGTTAA
Found at i:43318061 original size:18 final size:17
Alignment explanation
Indices: 43318008--43318068 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
43317998 AATTTATAAT
* *
43318008 TTTTTATTATGTTCATAA
1 TTTTTAATATTTTC-TAA
43318026 TTTATATAAT-TTTT-TAA
1 TTT-T-TAATATTTTCTAA
43318043 TATTTTAATATTTTCTAA
1 T-TTTTAATATTTTCTAA
43318061 TTTTTAAT
1 TTTTTAAT
43318069 TAATTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
16 4 0.11
17 16 0.44
18 9 0.25
19 4 0.11
20 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTAATATTTTCTAA
Found at i:43319031 original size:41 final size:41
Alignment explanation
Indices: 43318961--43319148 Score: 236
Period size: 42 Copynumber: 4.6 Consensus size: 41
43318951 ATAATAAATA
*
43318961 TATTTATTTTTTAATTTTAAAATATTTTTTACATACTTTTTTT
1 TATTT-TTTTTTAATTTTAAAATATTTTTTAAATAC-TTTTTT
*
43319004 TATTTTTTTTTAATTTTAAAATATTTTTTACATAC-TTTTT
1 TATTTTTTTTTAATTTTAAAATATTTTTTAAATACTTTTTT
* *
43319044 TA-TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTT
1 TATTTTTTTTTAATTTTAAAATATTTTTTAAATACTTTTTT
** **
43319084 TAAATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTT
1 TATTTTTTTTTAATTTTAAAATATTTTTTAAATACTTTTTT
***
43319125 TAATTTTTTAAAAATTTTAAAATA
1 T-ATTTTTTTTTAATTTTAAAATA
43319149 AAAATGGGCC
Statistics
Matches: 131, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 29 0.22
40 14 0.11
41 36 0.27
42 47 0.36
43 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (41 bp):
TATTTTTTTTTAATTTTAAAATATTTTTTAAATACTTTTTT
Found at i:43319043 original size:32 final size:33
Alignment explanation
Indices: 43319006--43319084 Score: 86
Period size: 39 Copynumber: 2.2 Consensus size: 33
43318996 CTTTTTTTTA
* *
43319006 TTTTTTTTTAATTTTAAAATATTTTTTACATAC
1 TTTTTTTTTAATTTTAAAATATTTTTAAAATAC
43319039 TTTTTTATTTTTTTAAATTTTAAAATATTTTTAAAATAC
1 ----TT-TTTTTTT-AATTTTAAAATATTTTTAAAATAC
43319078 TTTTTTT
1 TTTTTTT
43319085 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 5 0.13
35 2 0.05
37 2 0.05
38 7 0.18
39 22 0.58
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:43319072 original size:11 final size:11
Alignment explanation
Indices: 43319056--43319148 Score: 58
Period size: 11 Copynumber: 8.9 Consensus size: 11
43319046 TTTTTTTAAA
43319056 TTTTAAAATAT
1 TTTTAAAATAT
43319067 TTTTAAAATACTT
1 TTTTAAAATA--T
*
43319080 TTTTTAAAT-T
1 TTTTAAAATAT
*
43319090 TTTT----TAA
1 TTTTAAAATAT
43319097 TTTTAAAATAT
1 TTTTAAAATAT
*
43319108 TTTAAAAATACT
1 TTTTAAAATA-T
**
43319120 TTTTTTAAT-T
1 TTTTAAAATAT
43319130 TTTTAAAA-A-
1 TTTTAAAATAT
43319139 TTTTAAAATA
1 TTTTAAAATA
43319149 AAAATGGGCC
Statistics
Matches: 63, Mismatches: 9, Indels: 21
0.68 0.10 0.23
Matches are distributed among these distances:
6 1 0.02
7 4 0.06
9 8 0.13
10 13 0.21
11 21 0.33
12 7 0.11
13 9 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:43321152 original size:11 final size:12
Alignment explanation
Indices: 43321138--43321172 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
43321128 ACCAAAACAA
43321138 ACAAAAAAAA-T
1 ACAAAAAAAAGT
43321149 ACAAAAAAAAGT
1 ACAAAAAAAAGT
43321161 A-AAAAAAAAGT
1 ACAAAAAAAAGT
43321172 A
1 A
43321173 AGAAAGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.91
12 2 0.09
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.09
Consensus pattern (12 bp):
ACAAAAAAAAGT
Found at i:43329745 original size:16 final size:16
Alignment explanation
Indices: 43329711--43329745 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43329701 AGGGCTTAAT
* *
43329711 GTAATAATAATTTGTG
1 GTAATAATAATCTGCG
43329727 GTAATAATAATCTGCG
1 GTAATAATAATCTGCG
43329743 GTA
1 GTA
43329746 TGTTTTGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAATAATAATCTGCG
Found at i:43337939 original size:29 final size:29
Alignment explanation
Indices: 43337875--43337940 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
43337865 ATTTTGACTT
* * * *
43337875 ATTTGATTTCTTTTAATACTATAAGGACTA
1 ATTTGA-TTCATTTAATAATAGAAGAACTA
* *
43337905 AATTGATTCATTTAATAATAGAAGAATTA
1 ATTTGATTCATTTAATAATAGAAGAACTA
43337934 ATTTGAT
1 ATTTGAT
43337941 CCAAACCCTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (29 bp):
ATTTGATTCATTTAATAATAGAAGAACTA
Found at i:43339673 original size:25 final size:23
Alignment explanation
Indices: 43339614--43339678 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
43339604 TTTGATCAAA
*
43339614 TTATTTTT-TCTTT-TTATTTCT
1 TTATTTTTCTCTTTCTTATTCCT
*
43339635 TTATTTTCCT-TTTCTTATTCCCCT
1 TTATTTTTCTCTTTCTTATT--CCT
*
43339659 TTATTTTTCTCTTTCATATT
1 TTATTTTTCTCTTTCTTATT
43339679 GTTAACTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 10 0.29
22 6 0.17
24 11 0.31
25 8 0.23
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTTTTCTCTTTCTTATTCCT
Done.