Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 176 of 190
Found at i:29332084 original size:37 final size:35
Alignment explanation
Indices: 29332043--29332144 Score: 91
Period size: 41 Copynumber: 2.7 Consensus size: 35
29332033 AAAAAATAAA
29332043 ATAAAATAAAAATAATAATTATATATATTTGTATTAT
1 ATAAAATAAAAATAATAATTATATATATTT-TA-TAT
*
29332080 ATAAAATATTAAAATTATATATTTATATAATATTTTATAT
1 ATAAAATA--AAAA-TA-ATAATTATAT-ATATTTTATAT
* *
29332120 A-AAAATTATATATAATAATT-TATAT
1 ATAAAA-TAAAAATAATAATTATATAT
29332145 TAATAAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
34 2 0.04
35 3 0.05
36 5 0.09
37 10 0.18
38 2 0.04
39 8 0.15
40 8 0.15
41 11 0.20
42 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (35 bp):
ATAAAATAAAAATAATAATTATATATATTTTATAT
Found at i:29332102 original size:31 final size:31
Alignment explanation
Indices: 29332064--29332132 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
29332054 ATAATAATTA
* * *
29332064 TATATATTTGTATTATATAAAATATTAAAAT
1 TATATATTTATATAATATAAAATATAAAAAT
***
29332095 TATATATTTATATAATATTTTATATAAAAAT
1 TATATATTTATATAATATAAAATATAAAAAT
29332126 TATATAT
1 TATATAT
29332133 AATAATTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TATATATTTATATAATATAAAATATAAAAAT
Found at i:29332148 original size:13 final size:12
Alignment explanation
Indices: 29332100--29332150 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 12
29332090 AAAATTATAT
29332100 ATTTATATAATA
1 ATTTATATAATA
* *
29332112 TTTTATATAAAA
1 ATTTATATAATA
29332124 ATTATATATAATA
1 ATT-TATATAATA
29332137 ATTTATATTAATA
1 ATTTATA-TAATA
29332150 A
1 A
29332151 AAAATATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTATATAATA
Found at i:29332157 original size:25 final size:24
Alignment explanation
Indices: 29332104--29332159 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
29332094 TTATATATTT
* *
29332104 ATATAATATTTTATATAAAAATTAT
1 ATATAATAATTTATATAAAAA-TAA
29332129 ATATAATAATTTATATTAATAAA-AA
1 ATATAATAATTTATA-TAA-AAATAA
29332154 ATATAA
1 ATATAA
29332160 AAAAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 21 0.78
26 3 0.11
27 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAATAATTTATATAAAAATAA
Found at i:29332240 original size:18 final size:17
Alignment explanation
Indices: 29332214--29332257 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
29332204 AACTTTTAAA
*
29332214 TTATATTATTTTATATT
1 TTATATTATATTATATT
29332231 TTATATTTATATTATATT
1 TTATA-TTATATTATATT
*
29332249 TTAAATTAT
1 TTATATTAT
29332258 CATGTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:29332257 original size:23 final size:23
Alignment explanation
Indices: 29332214--29332257 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29332204 AACTTTTAAA
**
29332214 TTATATTATTTTATATTTTATAT
1 TTATATTATTTTATAAATTATAT
29332237 TTATATTATATTT-TAAATTAT
1 TTATATTAT-TTTATAAATTAT
29332258 CATGTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATATTATTTTATAAATTATAT
Found at i:29332585 original size:6 final size:6
Alignment explanation
Indices: 29332574--29332598 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29332564 CGTGTCAGCA
29332574 AAAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG A
29332599 TGGAGCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:29336766 original size:2 final size:2
Alignment explanation
Indices: 29336759--29336787 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29336749 GATTTTCTTC
29336759 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 T
29336788 TCATATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29337292 original size:22 final size:23
Alignment explanation
Indices: 29337253--29337301 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
29337243 CCATGATTTA
29337253 TATGGCACTTAATGTAATTCGTT
1 TATGGCACTTAATGTAATTCGTT
29337276 TATGGCACTT-ATGTAATTCGTT
1 TATGGCACTTAATGTAATTCGTT
29337298 TATG
1 TATG
29337302 TATTTTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (23 bp):
TATGGCACTTAATGTAATTCGTT
Found at i:29340565 original size:2 final size:2
Alignment explanation
Indices: 29340558--29340585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29340548 TGTATATGTC
29340558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29340586 CCCAACAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29342342 original size:25 final size:24
Alignment explanation
Indices: 29342306--29342358 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
29342296 TATTCAACAA
* *
29342306 TAAAAATTTTAT-CAAAATATTTAT
1 TAAAAATATTATCCAAAA-ATATAT
29342330 TAAAAATAATTATCCAAAAATATAT
1 TAAAAAT-ATTATCCAAAAATATAT
29342355 TAAA
1 TAAA
29342359 GTTATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAATATTATCCAAAAATATAT
Found at i:29344563 original size:2 final size:2
Alignment explanation
Indices: 29344556--29344603 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
29344546 GTTTGTGTAA
* * *
29344556 AT AT AT AT AT AT AT AT -T AT -T TT GT TT 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
29344596 AT AT AT AT
1 AT AT AT AT
29344604 TATTTTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:29344592 original size:32 final size:32
Alignment explanation
Indices: 29344556--29344617 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
29344546 GTTTGTGTAA
29344556 ATATATATATATATATTATTTTGTTTATATAT
1 ATATATATATATATATTATTTTGTTTATATAT
29344588 ATATATATATATATATTATTTTGTTTATAT
1 ATATATATATATATATTATTTTGTTTATAT
29344618 TAAATTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (32 bp):
ATATATATATATATATTATTTTGTTTATATAT
Found at i:29344617 original size:28 final size:29
Alignment explanation
Indices: 29344547--29344604 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
29344537 GTGATGTTTG
29344547 TTTGTGTAAATATATATATATATAT-TAT
1 TTTGTGTAAATATATATATATATATATAT
* *
29344575 TTTGTTTATATATATATATATATATATAT
1 TTTGTGTAAATATATATATATATATATAT
29344604 T
1 T
29344605 ATTTTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (29 bp):
TTTGTGTAAATATATATATATATATATAT
Found at i:29345378 original size:2 final size:2
Alignment explanation
Indices: 29345371--29345401 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29345361 TTCTTTCTCT
29345371 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
29345402 TAATATTAAG
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:29345813 original size:2 final size:2
Alignment explanation
Indices: 29345806--29345833 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29345796 CATTAATGTT
29345806 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29345834 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29345838 original size:2 final size:2
Alignment explanation
Indices: 29345833--29345867 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29345823 ATATATATAT
*
29345833 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29345868 CAAAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29348727 original size:64 final size:64
Alignment explanation
Indices: 29348624--29348751 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 64
29348614 TAGCAGAATG
*
29348624 TATGCCATCCATTTCGAAACTTCTACCCTGGGAACAGTTAAATCCCACAATTGTCATGTCAACC
1 TATGCCATCCATTTCGAAACTTCTACCCTGGGAACAGTTAAACCCCACAATTGTCATGTCAACC
* * * * *
29348688 TATGCCATCCATTTGGAAACTTCTA-TCTGGGGAAGAGTTAAACCCCTCAATTTTCATGTCAACC
1 TATGCCATCCATTTCGAAACTTCTACCCT-GGGAACAGTTAAACCCCACAATTGTCATGTCAACC
29348752 ACAGAAAGGC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 2 0.04
64 55 0.96
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (64 bp):
TATGCCATCCATTTCGAAACTTCTACCCTGGGAACAGTTAAACCCCACAATTGTCATGTCAACC
Found at i:29355060 original size:28 final size:27
Alignment explanation
Indices: 29355006--29355068 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
29354996 ATCAATCGTA
29355006 AATAT-TGAACAAATATATTCATAAAT
1 AATATATGAACAAATATATTCATAAAT
* * *
29355032 ATATATATGAACAAATATGTTTATGAAT
1 A-ATATATGAACAAATATATTCATAAAT
29355060 AATAATATG
1 AAT-ATATG
29355069 TTAATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.19
28 24 0.77
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (27 bp):
AATATATGAACAAATATATTCATAAAT
Found at i:29355068 original size:18 final size:18
Alignment explanation
Indices: 29355045--29355082 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29355035 TATATGAACA
* *
29355045 AATATGTTTATGAATAAT
1 AATATGTTAATAAATAAT
29355063 AATATGTTAATAAATAAT
1 AATATGTTAATAAATAAT
29355081 AA
1 AA
29355083 ACAACAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AATATGTTAATAAATAAT
Found at i:29355274 original size:25 final size:24
Alignment explanation
Indices: 29355222--29355275 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
29355212 TTATTATTAT
29355222 TGAATAATAAATAAATAAACTTTA
1 TGAATAATAAATAAATAAACTTTA
*
29355246 --AATAA-AAATAAATAAATTTTCAA
1 TGAATAATAAATAAATAAACTTT--A
29355269 TGAATAA
1 TGAATAA
29355276 GTTTTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
23 1 0.04
25 5 0.20
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
TGAATAATAAATAAATAAACTTTA
Found at i:29357778 original size:2 final size:2
Alignment explanation
Indices: 29357773--29357805 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29357763 ATTTTTTGAC
29357773 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 T
29357806 GGACATGCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29368724 original size:10 final size:10
Alignment explanation
Indices: 29368709--29368738 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29368699 TATCCCTTCA
29368709 TTCTCTCTCT
1 TTCTCTCTCT
29368719 TTCTCTCTCT
1 TTCTCTCTCT
*
29368729 CTCTCTCTCT
1 TTCTCTCTCT
29368739 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (10 bp):
TTCTCTCTCT
Found at i:29368743 original size:2 final size:2
Alignment explanation
Indices: 29368738--29368762 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29368728 TCTCTCTCTC
29368738 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
29368763 TTGCAGTACG
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:29369003 original size:22 final size:21
Alignment explanation
Indices: 29368968--29369008 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29368958 TTATCTTTAA
29368968 AATAATAAATTTAATTAAATG
1 AATAATAAATTTAATTAAATG
*
29368989 AATAATCATATTTAATTAAA
1 AATAAT-AAATTTAATTAAA
29369009 AAATTGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATAAATTTAATTAAATG
Found at i:29370951 original size:21 final size:20
Alignment explanation
Indices: 29370921--29370989 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
29370911 TGAATCGACG
*
29370921 ATAAGATTAATTTTGATGATA
1 ATAAAATTAATTTT-ATGATA
* *
29370942 TTAAAATTAA--TAATGATA
1 ATAAAATTAATTTTATGATA
*
29370960 ATAAAATTAATTATTATAATA
1 ATAAAATTAATT-TTATGATA
29370981 ATAAAATTA
1 ATAAAATTA
29370990 GAATTAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
21 23 0.59
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (20 bp):
ATAAAATTAATTTTATGATA
Found at i:29370957 original size:18 final size:18
Alignment explanation
Indices: 29370936--29370981 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
29370926 ATTAATTTTG
*
29370936 ATGATATTAAAATTAATA
1 ATGATAATAAAATTAATA
*
29370954 ATGATAATAAAATTAATT
1 ATGATAATAAAATTAATA
*
29370972 ATTATAATAA
1 ATGATAATAA
29370982 TAAAATTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
ATGATAATAAAATTAATA
Found at i:29370999 original size:21 final size:19
Alignment explanation
Indices: 29370943--29371002 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 19
29370933 TTGATGATAT
*
29370943 TAAAATTAA-TAATGATAA
1 TAAAATTAATTAATAATAA
29370961 TAAAATTAATTATTATAATAA
1 TAAAATTAATTA--ATAATAA
29370982 TAAAATTAGAATTAATAATAA
1 TAAAATT--AATTAATAATAA
29371003 AGAATACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 9 0.25
19 2 0.06
21 20 0.56
23 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TAAAATTAATTAATAATAA
Found at i:29381648 original size:2 final size:2
Alignment explanation
Indices: 29381641--29381671 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29381631 TTCAGTAATA
29381641 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 A
29381672 AAAACAAAGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29390782 original size:9 final size:9
Alignment explanation
Indices: 29390768--29390801 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
29390758 TGCTGCTGAA
29390768 GAAGAAGTG
1 GAAGAAGTG
**
29390777 GAAGAAGAA
1 GAAGAAGTG
29390786 GAAGAAGTG
1 GAAGAAGTG
29390795 GAAGAAG
1 GAAGAAG
29390802 GAGAAGGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (9 bp):
GAAGAAGTG
Found at i:29390788 original size:18 final size:18
Alignment explanation
Indices: 29390765--29390807 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
29390755 TGTTGCTGCT
29390765 GAAGAAGAAGTGGAAGAA
1 GAAGAAGAAGTGGAAGAA
29390783 GAAGAAGAAGTGGAAGAA
1 GAAGAAGAAGTGGAAGAA
*
29390801 GGAGAAG
1 GAAGAAG
29390808 GAGACAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAGTGGAAGAA
Found at i:29403408 original size:63 final size:63
Alignment explanation
Indices: 29403331--29403454 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
29403321 AGAATAATCA
*
29403331 GCATAATACAGTAACTAAAGAATTCCAAAACTGTGTTCATCTTATGACATGTAAGGAAAGACG
1 GCATAATACAGTAACTAAAGAATTCCAAAACTGTGTTCATCTTATGACATGCAAGGAAAGACG
* * * *
29403394 GCATAATAGAGTAACTAAAGAATTGCAAAGCTGTGTTCATCTTATTACATGCAAGGAAAGA
1 GCATAATACAGTAACTAAAGAATTCCAAAACTGTGTTCATCTTATGACATGCAAGGAAAGA
29403455 TTGTGCATAC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (63 bp):
GCATAATACAGTAACTAAAGAATTCCAAAACTGTGTTCATCTTATGACATGCAAGGAAAGACG
Found at i:29406585 original size:15 final size:15
Alignment explanation
Indices: 29406562--29406592 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29406552 GATTTGATTA
*
29406562 ATTTTAAATTAAATT
1 ATTTAAAATTAAATT
29406577 ATTTAAAATTAAATT
1 ATTTAAAATTAAATT
29406592 A
1 A
29406593 ATCAAATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAAAATTAAATT
Found at i:29406717 original size:16 final size:16
Alignment explanation
Indices: 29406692--29406724 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29406682 AACCAAATAA
29406692 TAAATATA-TTTAAAT
1 TAAATATATTTTAAAT
29406707 TAAATTATATTTTAAAT
1 TAAA-TATATTTTAAAT
29406724 T
1 T
29406725 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATATATTTTAAAT
Found at i:29406865 original size:7 final size:7
Alignment explanation
Indices: 29406832--29406880 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
29406822 AATATAATGA
29406832 ATTTTAT
1 ATTTTAT
*
29406839 ATATTTTT
1 AT-TTTAT
29406847 CATTTT-T
1 -ATTTTAT
29406854 CATTTTAT
1 -ATTTTAT
29406862 ATTTTAT
1 ATTTTAT
29406869 ATTTTAT
1 ATTTTAT
29406876 ATTTT
1 ATTTT
29406881 TTTATATTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
7 28 0.74
8 8 0.21
9 2 0.05
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTAT
Found at i:29406880 original size:21 final size:23
Alignment explanation
Indices: 29406832--29406873 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29406822 AATATAATGA
*
29406832 ATTTTATATATTTTTCATTTTTC
1 ATTTTATATATTTATCATTTTTC
29406855 ATTTTATAT-TTTAT-ATTTT
1 ATTTTATATATTTATCATTTT
29406874 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTTATATATTTATCATTTTTC
Found at i:29413855 original size:20 final size:20
Alignment explanation
Indices: 29413814--29413860 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29413804 TGCTTGTTTT
*
29413814 ATATTTTTTATATTTAATAA
1 ATATTTTTTAGATTTAATAA
29413834 ATATTTTTTAGGATTT--TAA
1 ATATTTTTTA-GATTTAATAA
29413853 A-ATTTTTT
1 ATATTTTTT
29413861 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 10 0.40
21 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATATTTTTTAGATTTAATAA
Found at i:29435272 original size:13 final size:13
Alignment explanation
Indices: 29435254--29435279 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29435244 AATCTATTTG
29435254 ATTTTAATTTTCA
1 ATTTTAATTTTCA
29435267 ATTTTAATTTTCA
1 ATTTTAATTTTCA
29435280 TTTAATCATT
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:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTAATTTTCA
Found at i:29438880 original size:22 final size:22
Alignment explanation
Indices: 29438855--29438905 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
29438845 ATAATTTTGT
*
29438855 TGGATTATTATTATTATTTGGA
1 TGGATTATTATTAATATTTGGA
29438877 TGGATTATTATTAATATTTGGA
1 TGGATTATTATTAATATTTGGA
29438899 T-GATTAT
1 TGGATTAT
29438906 CCAGACAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (22 bp):
TGGATTATTATTAATATTTGGA
Found at i:29439344 original size:15 final size:15
Alignment explanation
Indices: 29439326--29439455 Score: 116
Period size: 15 Copynumber: 8.7 Consensus size: 15
29439316 CCACCTAGCT
* *
29439326 CTCCTCCTCCAGCAA
1 CTCCTCCTCCGGCTA
* * *
29439341 CTCCACCACCGGCTT
1 CTCCTCCTCCGGCTA
*
29439356 CTCCTCCCCCGGCTA
1 CTCCTCCTCCGGCTA
* *
29439371 CTCCACCTCCGGCCA
1 CTCCTCCTCCGGCTA
*
29439386 CTCCTCCTCCGGCTT
1 CTCCTCCTCCGGCTA
* *
29439401 CTCCTCCTCAGGCCA
1 CTCCTCCTCCGGCTA
* * * *
29439416 CTCCACCACCTGCTT
1 CTCCTCCTCCGGCTA
*
29439431 CTCCTCCTCCTGCTA
1 CTCCTCCTCCGGCTA
29439446 CTCCTCCTCC
1 CTCCTCCTCC
29439456 AGCAACCCCA
Statistics
Matches: 89, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 89 1.00
ACGTcount: A:0.10, C:0.56, G:0.10, T:0.24
Consensus pattern (15 bp):
CTCCTCCTCCGGCTA
Found at i:29439362 original size:45 final size:45
Alignment explanation
Indices: 29439313--29439407 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
29439303 AGTTTCAACC
* *
29439313 CCTCCACCTAGCT-CTCCTCCTCCAGCAACTCCACCACCGGCTTCT
1 CCTCC-CCCAGCTACTCCACCTCCAGCAACTCCACCACCGGCTTCT
* * * * *
29439358 CCTCCCCCGGCTACTCCACCTCCGGCCACTCCTCCTCCGGCTTCT
1 CCTCCCCCAGCTACTCCACCTCCAGCAACTCCACCACCGGCTTCT
29439403 CCTCC
1 CCTCC
29439408 TCAGGCCACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 5 0.12
45 37 0.88
ACGTcount: A:0.11, C:0.57, G:0.11, T:0.22
Consensus pattern (45 bp):
CCTCCCCCAGCTACTCCACCTCCAGCAACTCCACCACCGGCTTCT
Found at i:29439419 original size:45 final size:45
Alignment explanation
Indices: 29439326--29439454 Score: 132
Period size: 45 Copynumber: 2.9 Consensus size: 45
29439316 CCACCTAGCT
* * * * * *
29439326 CTCCTCCTCCAGCAACTCCACCACCGGCTTCTCCTCCCCCGGCTA
1 CTCCACCTCCAGCAACTCCTCCTCCGGCTTCTCCTCCTCAGGCCA
* *
29439371 CTCCACCTCCGGCCACTCCTCCTCCGGCTTCTCCTCCTCAGGCCA
1 CTCCACCTCCAGCAACTCCTCCTCCGGCTTCTCCTCCTCAGGCCA
* * ** * *
29439416 CTCCACCACCTGCTTCTCCTCCTCCTGCTACTCCTCCTC
1 CTCCACCTCCAGCAACTCCTCCTCCGGCTTCTCCTCCTC
29439455 CAGCAACCCC
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.10, C:0.56, G:0.10, T:0.24
Consensus pattern (45 bp):
CTCCACCTCCAGCAACTCCTCCTCCGGCTTCTCCTCCTCAGGCCA
Found at i:29444644 original size:1 final size:1
Alignment explanation
Indices: 29444638--29444662 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29444628 CAAAATCCTG
29444638 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
29444663 GTTTCTTCTG
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:29449171 original size:5 final size:5
Alignment explanation
Indices: 29449161--29449185 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29449151 GGAACTGCAT
29449161 AGCAG AGCAG AGCAG AGCAG AGCAG
1 AGCAG AGCAG AGCAG AGCAG AGCAG
29449186 TGGGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
AGCAG
Found at i:29451636 original size:11 final size:11
Alignment explanation
Indices: 29451604--29451637 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29451594 TAGTATTATT
*
29451604 ATAAATAAACA
1 ATAAATAAATA
29451615 ATAAATAAATA
1 ATAAATAAATA
*
29451626 ATAAATGAATA
1 ATAAATAAATA
29451637 A
1 A
29451638 AATTTGTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:29451922 original size:4 final size:4
Alignment explanation
Indices: 29451907--29451935 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
29451897 ATCTTACTCG
29451907 AATT AATT -ATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
29451936 ATCGAGTTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:29454002 original size:28 final size:28
Alignment explanation
Indices: 29453971--29454025 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
29453961 ATTTTAAATT
29453971 TAGTTATTAATTTATTAATGAATGACAC
1 TAGTTATTAATTTATTAATGAATGACAC
*
29453999 TAGTTATTAATTTATTATTGAATGACA
1 TAGTTATTAATTTATTAATGAATGACA
29454026 ATCTGTCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (28 bp):
TAGTTATTAATTTATTAATGAATGACAC
Found at i:29454594 original size:11 final size:11
Alignment explanation
Indices: 29454578--29454603 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29454568 ATAATAAAAT
29454578 ATTTGTATTTA
1 ATTTGTATTTA
29454589 ATTTGTATTTA
1 ATTTGTATTTA
29454600 ATTT
1 ATTT
29454604 AATTAAATTA
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:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
ATTTGTATTTA
Found at i:29454648 original size:23 final size:23
Alignment explanation
Indices: 29454610--29454718 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 23
29454600 ATTTAATTAA
* * *
29454610 ATTAAATAAGTTTATTCGTAAAT
1 ATTAAATAAATATATTCATAAAT
*
29454633 ATTAAATAAATATATTTATAAAT
1 ATTAAATAAATATATTCATAAAT
* *
29454656 ATTTATAAACAAATATATTTATAAAT
1 A--T-TAAATAAATATATTCATAAAT
* * * *
29454682 AATAAACAAACCATAATCAAATAAAT
1 ATTAAATAAA-TATATTC--ATAAAT
29454708 -TTAAATAAATA
1 ATTAAATAAATA
29454719 AACTCTAAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
23 28 0.41
24 5 0.07
25 8 0.12
26 27 0.40
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTAAATAAATATATTCATAAAT
Found at i:29456246 original size:29 final size:29
Alignment explanation
Indices: 29456189--29456246 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
29456179 AAATATAAAA
* **
29456189 TATAATTTTTTAATTTTATTAAATTTATT
1 TATAATTTTTAAAAATTATTAAATTTATT
29456218 TATAATTTTTAAAAATT-TTAAATTATATT
1 TATAATTTTTAAAAATTATTAAATT-TATT
29456247 ATCTTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATAATTTTTAAAAATTATTAAATTTATT
Found at i:29456927 original size:25 final size:28
Alignment explanation
Indices: 29456877--29456936 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
29456867 ACAAGTTAAA
*
29456877 AATAATTTGTATATATATATATATA-TT
1 AATATTTTGTATATATATATATATATTT
29456904 AATATTTTGTATATA-ATATA-ATATTT
1 AATATTTTGTATATATATATATATATTT
29456930 AA-ATTTT
1 AATATTTT
29456937 CTTTTATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 8 0.26
26 9 0.29
27 14 0.45
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATATTTTGTATATATATATATATATTT
Found at i:29457833 original size:20 final size:19
Alignment explanation
Indices: 29457795--29457833 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29457785 TCATTAAAAA
29457795 TAAATAAATCTTAATTAAT
1 TAAATAAATCTTAATTAAT
* *
29457814 TAAATTAATCATTTATTAAT
1 TAAATAAATC-TTAATTAAT
29457834 ATTTACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATAAATCTTAATTAAT
Found at i:29460343 original size:55 final size:55
Alignment explanation
Indices: 29460278--29460390 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
29460268 ACATCATGTT
* *
29460278 TCTTTCTCTTTCGGTGACAGTTTATACTTCTTTGTTTATGGTTGTGCGAGTTTTA
1 TCTTTCTCTTTCGGTGACAGTTTATACTTCTTTGTTTATGGTTGTGCAAGTTTAA
*
29460333 TCTTTCTCTTTTGGTGACAGTTTATACTTCTTTGTTTATGGTTGTGCAAGTTTAA
1 TCTTTCTCTTTCGGTGACAGTTTATACTTCTTTGTTTATGGTTGTGCAAGTTTAA
29460388 TCT
1 TCT
29460391 GATAATTATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (55 bp):
TCTTTCTCTTTCGGTGACAGTTTATACTTCTTTGTTTATGGTTGTGCAAGTTTAA
Found at i:29460385 original size:30 final size:29
Alignment explanation
Indices: 29460295--29460386 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 29
29460285 CTTTCGGTGA
29460295 CAGTTTATACTTCTTTGTTTATGGTTGTG
1 CAGTTTATACTTCTTTGTTTATGGTTGTG
* * *
29460324 CGAGTTT-TA--TCTTTCTCTTTTGG-TG-A
1 C-AGTTTATACTTCTTTGT-TTATGGTTGTG
29460350 CAGTTTATACTTCTTTGTTTATGGTTGTG
1 CAGTTTATACTTCTTTGTTTATGGTTGTG
29460379 CAAGTTTA
1 C-AGTTTA
29460387 ATCTGATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
25 5 0.10
26 3 0.06
27 13 0.27
28 13 0.27
29 4 0.08
30 11 0.22
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53
Consensus pattern (29 bp):
CAGTTTATACTTCTTTGTTTATGGTTGTG
Found at i:29470521 original size:57 final size:57
Alignment explanation
Indices: 29470427--29470540 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
29470417 TTGGCTGTAC
*
29470427 ATCATTTGTTCATGTTCACAGCCATAATAGAGAAAAGTTGGATCCAAGAGCGATTAA
1 ATCATTTGTTCATGTTCACAGCCATAACAGAGAAAAGTTGGATCCAAGAGCGATTAA
* * *
29470484 ATCATTTGTTCATGTTCACAGTCATAACAGGGGAAAGTTGGATCCAAGAGCGATTAA
1 ATCATTTGTTCATGTTCACAGCCATAACAGAGAAAAGTTGGATCCAAGAGCGATTAA
29470541 GTGTATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (57 bp):
ATCATTTGTTCATGTTCACAGCCATAACAGAGAAAAGTTGGATCCAAGAGCGATTAA
Found at i:29474545 original size:18 final size:19
Alignment explanation
Indices: 29474522--29474568 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
29474512 TTATGTTATG
29474522 TAATATTTATATAAAATA-
1 TAATATTTATATAAAATAT
* *
29474540 TAATATAAATATATAAATTAT
1 TAATAT--TTATATAAAATAT
29474561 TAATATTT
1 TAATATTT
29474569 GACGTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 6 0.26
19 1 0.04
20 10 0.43
21 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATTTATATAAAATAT
Found at i:29479789 original size:2 final size:2
Alignment explanation
Indices: 29479782--29479810 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29479772 CAAAACTGAA
29479782 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 A
29479811 ATCTTACCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29481387 original size:2 final size:2
Alignment explanation
Indices: 29481382--29481424 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
29481372 CGTGTGTATG
* * * *
29481382 TA TA TA TA TA TA TA TA TA CA TA TA TA TT TG TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29481424 T
1 T
29481425 TATGATCCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:29488866 original size:12 final size:12
Alignment explanation
Indices: 29488851--29488875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29488841 ATAAATACTA
29488851 TAAATAATATTT
1 TAAATAATATTT
29488863 TAAATAATATTT
1 TAAATAATATTT
29488875 T
1 T
29488876 CATTCTCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATAATATTT
Found at i:29495742 original size:21 final size:21
Alignment explanation
Indices: 29495718--29495762 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
29495708 AAATTTTTTT
29495718 ATTAAAAATAATTAAA-TAAAA
1 ATTAAAAATAA-TAAATTAAAA
*
29495739 ATTAAAATTAATAAATTAAAA
1 ATTAAAAATAATAAATTAAAA
29495760 ATT
1 ATT
29495763 TTTATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAAATAATAAATTAAAA
Found at i:29496033 original size:13 final size:13
Alignment explanation
Indices: 29496017--29496055 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
29496007 ATTTTTCGAT
29496017 TTAAATTTTTTTA
1 TTAAATTTTTTTA
*
29496030 TTAAA-GTTTTTA
1 TTAAATTTTTTTA
29496042 TTAAATTATTTTTA
1 TTAAATT-TTTTTA
29496056 AGAAAATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 11 0.50
13 5 0.23
14 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TTAAATTTTTTTA
Found at i:29505484 original size:357 final size:358
Alignment explanation
Indices: 29504826--29505574 Score: 959
Period size: 357 Copynumber: 2.1 Consensus size: 358
29504816 CGCATTGAAC
* * *
29504826 ATATCGTTACACAAATTCTAACACTGTTATTGAAGGCATATATCCAAGAAAAATGCCTTTAATAA
1 ATATCGTCACACAAATTGTAACACTGTTATTGAAAGCATATATCCAAGAAAAATGCCTTTAATAA
* ** * * * *
29504891 TTTCTATCACAATTTGTAGTTAATTACTGAAGGCAGTTGCAGAAAATAATGCCTTTAATAATTTC
66 TTCCTATCACAATTTGTAGTTAAACACTGAAGGCAATTGCAGAAAACAACGCCTTCAATAATTTC
* * * *
29504956 CCTAAAAAAAATTTCTCAAATTATTAAAGGCAGTCTTTTATTATAAGACGCCTTCAATATACTAC
131 CCTAAAAAAAATTTCTCAAATTATTAAAAGCAGTCTTTTATTATAAAACACCTTCAATATACCAC
* *
29505021 GATAGTAATGGAAGGTATTTATTAGAAATGACACCTTCAATATATCTTTAAACTTAGAAATCTAT
196 GATAGTAATGGAAGGTATTTATTAGAAATGACACCTTCAATATACCTTTAAACTTAGAAATCCAT
* * *
29505086 TACTGAAGGCATTTGTTAATAATAGACGCCTTCATAATTTTTTCACTTAATATTTTAAAAATTAT
261 TACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTTCACTAAATATTTTAAAAATTAT
***
29505151 TAAAGGTATATTCTACTGTAAAATACCTTCTAT
326 TAAAAACATATTCTACTGTAAAATACCTTCTAT
* * ** **
29505184 ATATCGTCACATAAATTGTAACATTGTTATTGAAAGCATATATTTAAGCTAAATGCCTTTAATAA
1 ATATCGTCACACAAATTGTAACACTGTTATTGAAAGCATATATCCAAGAAAAATGCCTTTAATAA
* * **
29505249 TTCCTATCATAGTTTGTA-TATAAACACTGAAGGCAATTTTAGAAAACAACGCCTTCAATAATTT
66 TTCCTATCACAATTTGTAGT-TAAACACTGAAGGCAATTGCAGAAAACAACGCCTTCAATAATTT
* * * *
29505313 TCTTAAAAAAAAAATTT-T-GAATTATTAAAAGCA-TCTTTTATTATAAAACACCTTTAATATAC
130 CCCT--AAAAAAAATTTCTCAAATTATTAAAAGCAGTCTTTTATTATAAAACACCTTCAATATAC
* * * * * *
29505375 CATGATGGTAATGGAAGGTGTTTATTAGAAAATG-CGCTTTCAATATACCTTTAAACTTAGTAAT
193 CACGATAGTAATGGAAGGTATTTATTAG-AAATGACACCTTCAATATACCTTTAAACTTAGAAAT
* * * * *
29505439 CCATTACTGAAGGCGTTTGTTAATAACAGATGCCTTTAAAATTTTTTCACTAAATATTTTGAGAA
257 CCATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTTCACTAAATATTTTAAAAA
* * *
29505504 TTATTAAAAACGTCTTCTACTGTAAAATACTTTCTAT
322 TTATTAAAAACATATTCTACTGTAAAATACCTTCTAT
* *
29505541 ATACCGTCACACAAATTGTAACACTATTATTGAA
1 ATATCGTCACACAAATTGTAACACTGTTATTGAA
29505575 CGCTTTTAAC
Statistics
Matches: 333, Mismatches: 54, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
357 194 0.58
358 127 0.38
359 1 0.00
360 11 0.03
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (358 bp):
ATATCGTCACACAAATTGTAACACTGTTATTGAAAGCATATATCCAAGAAAAATGCCTTTAATAA
TTCCTATCACAATTTGTAGTTAAACACTGAAGGCAATTGCAGAAAACAACGCCTTCAATAATTTC
CCTAAAAAAAATTTCTCAAATTATTAAAAGCAGTCTTTTATTATAAAACACCTTCAATATACCAC
GATAGTAATGGAAGGTATTTATTAGAAATGACACCTTCAATATACCTTTAAACTTAGAAATCCAT
TACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTTCACTAAATATTTTAAAAATTAT
TAAAAACATATTCTACTGTAAAATACCTTCTAT
Found at i:29513616 original size:21 final size:21
Alignment explanation
Indices: 29513592--29513644 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
29513582 AGAATATAAG
29513592 CGTGCCAAAATTGAAGAAGAA
1 CGTGCCAAAATTGAAGAAGAA
* * * * *
29513613 CGTGCTAGAATGGAGGTAGAA
1 CGTGCCAAAATTGAAGAAGAA
29513634 CGTG-CAAAATT
1 CGTGCCAAAATT
29513645 TTAGTAATTG
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (21 bp):
CGTGCCAAAATTGAAGAAGAA
Found at i:29516262 original size:156 final size:155
Alignment explanation
Indices: 29516001--29516311 Score: 604
Period size: 156 Copynumber: 2.0 Consensus size: 155
29515991 CTTTTTCATT
29516001 TTTCTCTGTCTATCTTTGTTTGGTTGGTGAGAAAATCCTGGTTAAAAAAAAAAAAAAGGACGCGG
1 TTTCTCTGTCTATCTTTGTTTGGTTGGTGAGAAAATCCTGGTTAAAAAAAAAAAAAAGGACGCGG
29516066 AAGTTTTCAAACCTTTTTTCATTTTTTCTTTGCGAAGTTGATGATCTTATCTTAGGTTACTATTG
66 AAGTTTTCAAACCTTTTTTCATTTTTTCTTTGCGAAGTTGATGATCTTATCTTAGGTTACTATTG
29516131 TGGGCTCAGTTTAGGTTTTATTTAC
131 TGGGCTCAGTTTAGGTTTTATTTAC
29516156 TTTCTCTGTCTATCTTTGTTTGGTTGGTGAGAAAATCCTGGTTAAAAAAAAAAAAAAAGGACGCG
1 TTTCTCTGTCTATCTTTGTTTGGTTGGTGAGAAAATCCTGGTT-AAAAAAAAAAAAAAGGACGCG
*
29516221 GAAGTTTTCAAACTTTTTTTCATTTTTTCTTTGCGAAGTTGATGATCTTATCTTAGGTTACTATT
65 GAAGTTTTCAAACCTTTTTTCATTTTTTCTTTGCGAAGTTGATGATCTTATCTTAGGTTACTATT
29516286 GTGGGCTCAGTTTAGGTTTTATTTAC
130 GTGGGCTCAGTTTAGGTTTTATTTAC
29516312 GTAAGTTCTC
Statistics
Matches: 154, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
155 43 0.28
156 111 0.72
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (155 bp):
TTTCTCTGTCTATCTTTGTTTGGTTGGTGAGAAAATCCTGGTTAAAAAAAAAAAAAAGGACGCGG
AAGTTTTCAAACCTTTTTTCATTTTTTCTTTGCGAAGTTGATGATCTTATCTTAGGTTACTATTG
TGGGCTCAGTTTAGGTTTTATTTAC
Found at i:29519876 original size:28 final size:28
Alignment explanation
Indices: 29519840--29519895 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
29519830 TTAGATTGAT
* *
29519840 TCCATAATCAGATATTATAGATTTATAA
1 TCCACAATCAGATATTACAGATTTATAA
*
29519868 TCCACAATCAGTTATTACAGATTTATAA
1 TCCACAATCAGATATTACAGATTTATAA
29519896 CTTGTTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (28 bp):
TCCACAATCAGATATTACAGATTTATAA
Found at i:29522531 original size:3 final size:3
Alignment explanation
Indices: 29522523--29522555 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29522513 AGTCTACTTG
29522523 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29522556 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29527298 original size:7 final size:8
Alignment explanation
Indices: 29527279--29527305 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29527269 TTAGTCTTTT
29527279 TTTTTTAA
1 TTTTTTAA
29527287 TTTTTTAA
1 TTTTTTAA
29527295 TTTTTTAA
1 TTTTTTAA
29527303 TTT
1 TTT
29527306 CATCACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTAA
Found at i:29539088 original size:28 final size:28
Alignment explanation
Indices: 29539052--29539107 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
29539042 TTAGATTGAT
* *
29539052 TCCATAATCAGATATTATAGATTTATAA
1 TCCACAATCAGATATTACAGATTTATAA
*
29539080 TCCACAATCAGTTATTACAGATTTATAA
1 TCCACAATCAGATATTACAGATTTATAA
29539108 CTTGTTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (28 bp):
TCCACAATCAGATATTACAGATTTATAA
Found at i:29541742 original size:3 final size:3
Alignment explanation
Indices: 29541734--29541760 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29541724 AGTCTACTTG
29541734 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
29541761 TAAAAAAAAA
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):
AAT
Found at i:29547285 original size:21 final size:20
Alignment explanation
Indices: 29547235--29547285 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
29547225 ATATTTGCCT
*
29547235 AAATACA-ACTTTTTTATATT
1 AAATACATA-TTTTTTATATC
29547255 AATATA-ATATTTATTTATATC
1 AA-ATACATATTT-TTTATATC
29547276 AAATACATAT
1 AAATACATAT
29547286 AAAATATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATACATATTTTTTATATC
Found at i:29558131 original size:34 final size:34
Alignment explanation
Indices: 29558095--29558158 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
29558085 AGTGTAATTA
*
29558095 AAAACTTTTTA-AAATATATTTTCAAAAAATTTT
1 AAAACTTTTTAGAAATAAATTTTCAAAAAATTTT
* * *
29558128 AAAAGTTTTTAGATATAAATTTTTAAAAAAT
1 AAAACTTTTTAGAAATAAATTTTCAAAAAAT
29558159 GTAAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 10 0.38
34 16 0.62
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
AAAACTTTTTAGAAATAAATTTTCAAAAAATTTT
Found at i:29560890 original size:5 final size:5
Alignment explanation
Indices: 29560882--29560914 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
29560872 ATATGATATA
29560882 ATAAT ATAAT ATAA- A-AAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
29560915 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.08
4 2 0.08
5 22 0.85
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:29560893 original size:13 final size:13
Alignment explanation
Indices: 29560871--29560910 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
29560861 GATAATCTAC
*
29560871 AATATGATATAAT
1 AATATAATATAAT
*
29560884 AATATAATATAAA
1 AATATAATATAAT
29560897 AATATAATATAAT
1 AATATAATATAAT
29560910 A
1 A
29560911 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:29560912 original size:23 final size:23
Alignment explanation
Indices: 29560882--29560957 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
29560872 ATATGATATA
29560882 ATAATATAATATAAAAATATAAT
1 ATAATATAATATAAAAATATAAT
* *
29560905 ATAATATAATTTAAAATTATAAT
1 ATAATATAATATAAAAATATAAT
* * * *
29560928 A-ATTATTATATATAAATTTAAT
1 ATAATATAATATAAAAATATAAT
*
29560950 AAAATATA
1 ATAATATA
29560958 TTTTATATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
22 16 0.38
23 26 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATATAATATAAAAATATAAT
Found at i:29560956 original size:45 final size:44
Alignment explanation
Indices: 29560878--29560962 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
29560868 TACAATATGA
*
29560878 TATAATAATATAATATAAAAATATAATATAATATAATTTAAAAT
1 TATAATAATATAATATAAAAATATAATAAAATATAATTTAAAAT
* * * *
29560922 TATAATAATTATTATATATAAATTTAATAAAATATATTTTA
1 TATAATAA-TATAATATAAAAATATAATAAAATATAATTTA
29560963 TATTTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (44 bp):
TATAATAATATAATATAAAAATATAATAAAATATAATTTAAAAT
Found at i:29560964 original size:23 final size:23
Alignment explanation
Indices: 29560896--29560964 Score: 56
Period size: 25 Copynumber: 3.0 Consensus size: 23
29560886 TATAATATAA
* * *
29560896 AAATATAATATAATATAATTTA-
1 AAATTTAATAAAATATATTTTAT
29560918 AAA-TT-ATAATAAT-TATTATATAT
1 AAATTTAATAA-AATATATT-T-TAT
29560941 AAATTTAATAAAATATATTTTAT
1 AAATTTAATAAAATATATTTTAT
29560964 A
1 A
29560965 TTTTATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
20 6 0.16
21 5 0.14
22 5 0.14
23 7 0.19
24 6 0.16
25 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATTTAATAAAATATATTTTAT
Found at i:29564390 original size:18 final size:18
Alignment explanation
Indices: 29564367--29564401 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29564357 TTAGTAAATT
29564367 TAAGAAAA-ACAAAAATAG
1 TAAGAAAATA-AAAAATAG
29564385 TAAGAAAATAAAAAATA
1 TAAGAAAATAAAAAATA
29564402 TGGCTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAGAAAATAAAAAATAG
Found at i:29566243 original size:36 final size:36
Alignment explanation
Indices: 29566197--29566268 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
29566187 ATTTTTTTTA
29566197 ATACTTTAAAAATGTTAAAATTTAAATTTTTATCAT
1 ATACTTTAAAAATGTTAAAATTTAAATTTTTATCAT
*
29566233 ATACTTTAAAATTGTTAAAATTTAAATTTTTATCAT
1 ATACTTTAAAAATGTTAAAATTTAAATTTTTATCAT
29566269 TAAAATTTTA
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:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (36 bp):
ATACTTTAAAAATGTTAAAATTTAAATTTTTATCAT
Found at i:29566574 original size:23 final size:22
Alignment explanation
Indices: 29566548--29566590 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
29566538 ACATCTAAAA
*
29566548 TTTTTATTTTTTTATAGTTAATT
1 TTTTTATTTTTTGATA-TTAATT
29566571 TTTTTATTTTTTGATATTAA
1 TTTTTATTTTTTGATATTAA
29566591 AAATCGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTTTATTTTTTGATATTAATT
Found at i:29574028 original size:10 final size:10
Alignment explanation
Indices: 29573988--29574027 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
29573978 GGTGCAATTA
29573988 AAAAAATTTT
1 AAAAAATTTT
29573998 AAATAAATTTT
1 AAA-AAATTTT
29574009 AAAAAATTTT
1 AAAAAATTTT
29574019 -AAAAATTTT
1 AAAAAATTTT
29574028 TTGGACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.31
10 10 0.34
11 10 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:29574166 original size:625 final size:613
Alignment explanation
Indices: 29572955--29574745 Score: 1997
Period size: 626 Copynumber: 2.9 Consensus size: 613
29572945 AGTAGCGCAG
*
29572955 AATGTGGGTTCCTTCTTTCCCCTTTTTTT-TTTT-TTTTTTTGCATAATGATGGATGATACCCAA
1 AATGTGGGTTCCTTCTTT--CGTTTTTTTCTTTTGTTTTTTTGCATAATGAT--A-G-TACCCAA
*
29573018 GAAAAGATT-TTTTTTTTTTTAATGATACTAATTGCATTT-C-AGTTTCCTCTCTTCATACCTCA
60 GAAAAGATTGTTTTTTTTTTTAATGATACTGATTGC-TTTCCAAG-TTCCTCTCTTCATACCTCA
* * * *
29573080 TTATTATTAGTACTTAATTTTTTACTTAATATAATCCTAATTTAAAATACAAATTTATTAAAAAT
123 TTATTGTTAATACTTAATTTTTTACTCAATATAATCCCAATTTAAAATACAAATTTA--AAAAAT
* ** * * * *
29573145 CCAAATAACTCATCTTCTTACAATCTATCTTTTCTCTATTTCCAACATAAAACCTAATGGATTTT
186 TCAAA-AAC-CATC-TCCCACAATC-ATCTTTTC-CTATTCCCAACCTAAAATCTAAAGGATTTT
* *
29573210 AAATCC-CAATCTAGTCAAATTCAAAGAAAATTTCAACCATTTAAGTTAAAAGACATAAAATTAA
246 AAA-CCTCAATCTAATCAAATTCAAAGAAAATTTCAACCATTTAAGTTAAAAAACATAAAATTAA
* * *
29573274 AGAT-AA--ATCT-TTTTTTTAATTTTTTATTTGA-TTTCATATTTAATTTCATAAGATTAAGAT
310 AGATAAATTATTTATTTTTTTTATTTTTTATTTGACTTT-GTATTTAATTTCATAAGATTAAGAT
* * * * * **
29573334 TTCATATCAAAATATTTGGATGTAATTAAAAACTTTTTAAAATAAATTTTCAAACGTTCTTAAAA
374 TTCATGTCGAAATATTTGGGTGCAATTAAAAACTTTTTAAAATAAATTTTAAAAAATT-TTAAAA
* *
29573399 ATTTTTGAACAAGAATTTTTAAAAGAAAATATAAAAAATAAAAAATTAATTAATTAA-AAAGTAT
438 ATTTTTGAACATGAATTTTTATAA-AAAATATAAAAAATAAAAAATTAATTAATTAATAAA-TAT
* *
29573463 TTAAATAATTTTATTAAAAATTAAATTTTTT-AATGTATTGATAAGAGGTTGAAGTGCAAATAAC
501 TTAAATAATTTCATT-AAAATTAAATTTTTTGAATGTATTGATAA-AAGTTG-AGTGCAAATAAC
* * * *
29573527 AATACTTTTTTTTTTAATCATTGCTCAGCGTCATTCCTTTAAATTTTTACT
563 AACACTCTTTTTTTTAATCATTGCTCAACGTCATTCCTTTAAATTATTACT
* *
29573578 AGTGTGGGTTCCTTCTTCTCGTTTTTTTTCTTTTGTTTTTTTGTATAATGATAGTACCCAAGAAA
1 AATGTGGGTTCCTTCTT-TCG-TTTTTTTCTTTTGTTTTTTTGCATAATGATAGTACCCAAGAAA
* * * * *
29573643 AGATTGTTTTTGTTTTTAACGATAGTGATTGCTTTCCAAGTTCCTCTCTTCGTACCTTATTATTG
64 AGATTGTTTTTTTTTTTAATGATACTGATTGCTTTCCAAGTTCCTCTCTTCATACCTCATTATTG
* * * *
29573708 TTAATATTTAATTTTTTGCTCGACATAATCCCAATTTAAAATACAAATTTACCAAAAATTCAAAC
129 TTAATACTTAATTTTTTACTCAATATAATCCCAATTTAAAATACAAATTTA--AAAAATTCAAA-
29573773 AATCCATCTCCCCACAATTCATCTTTTCCCTATTCCCAACCTAAAATCTAAAGGATTTTAAACCT
191 AA-CCATCT-CCCACAA-TCATCTTTT-CCTATTCCCAACCTAAAATCTAAAGGATTTTAAACCT
* *
29573838 CAATCTAAACAAATTCAAAG-AAATTTTAACCATTTAAGTTAAAAAACATAAAATTAAAGATAAA
252 CAATCTAATCAAATTCAAAGAAAATTTCAACCATTTAAGTTAAAAAACATAAAATTAAAGATAAA
* * *
29573902 TTATTTATTCTTTTTTATTTTTTATTTGACTTTGTATTTAATTTCGTAAGATTAATATTTTATGT
317 TTATTTATT-TTTTTTATTTTTTATTTGACTTTGTATTTAATTTCATAAGATTAAGATTTCATGT
* **
29573967 CGCAATATTTGGGTGCAATTAAAAAAATTTT-AAATAAATTTTAAAAAATTTTAAAAATTTTTTG
381 CGAAATATTTGGGTGCAATTAAAAACTTTTTAAAATAAATTTTAAAAAATTTTAAAAA-TTTTTG
* *
29574031 GACATGTAATTTTTTTAAAAAATATAAAAAATATAAAAA-TAATTAATTAATAAATATTTAAATA
445 AACATG-AATTTTTATAAAAAATATAAAAAATA-AAAAATTAATTAATTAATAAATATTTAAATA
* * *
29574095 ATTTCATTAAAGATTAAATTTTTTGACTATATTAATAAAATGTTGAGTGCAAATAACAACACTCT
508 ATTTCATTAAA-ATTAAATTTTTTGAATGTATTGATAAAA-GTTGAGTGCAAATAACAACACTCT
*
29574160 TTTTTTTAGTCATTGCTCAACGTCATTCCTTTAAATTATTACT
571 TTTTTTTAATCATTGCTCAACGTCATTCCTTTAAATTATTACT
** *
29574203 AATGTGGGTTCCTTCTTTTCGTTTTTTTCTTTTG-TTTTTTGCATAATGACGGTACCCAAGATAA
1 AATGTGGGTTCCTTC-TTTCGTTTTTTTCTTTTGTTTTTTTGCATAATGATAGTACCCAAGAAAA
* * * * *
29574267 GATTGTTTTTTTTTTTTTAAATGATATTGATTGCATTCCAACTTCCTCTCTTCATAGCTCACTAT
65 GATTG--TTTTTTTTTTT-AATGATACTGATTGCTTTCCAAGTTCCTCTCTTCATACCTCATTAT
*
29574332 TGTTAATACTTAATTTTTCACTCAATATAATCCCAATTTAAAATACAAATTT-----A-T-AAAA
127 TGTTAATACTTAATTTTTTACTCAATATAATCCCAATTTAAAATACAAATTTAAAAAATTCAAAA
* *
29574390 A--A--T-CCA-AA-CA---------A--CCCATCCTAAAATATAAAGGATTTTAAA-CTCCAAT
192 ACCATCTCCCACAATCATCTTTTCCTATTCCCAACCTAAAATCTAAAGGATTTTAAACCT-CAAT
* *
29574436 CTAATCAAATTCAAAGAAAATTTCAACCATTGAAGTTAAAAAATATAAAATTAAAGATAAATTAT
256 CTAATCAAATTCAAAGAAAATTTCAACCATTTAAGTTAAAAAACATAAAATTAAAGATAAATTAT
* * *
29574501 TTA----TTAT-TTTTTTATTT-AATTTCGTATTTAATTTCATAAAATTAAGATTTCATGTCGAA
321 TTATTTTTTTTATTTTTTATTTGACTTT-GTATTTAATTTCATAAGATTAAGATTTCATGTCGAA
* * *
29574560 ATATTTGTGTGCAATTAAAAACTTTTTAAAAATAAATTTTTAAAAATTTTTAAAAATTTTCGAAC
385 ATATTTGGGTGCAATTAAAAACTTTTT-AAAATAAA-TTTTAAAAAATTTTAAAAATTTTTGAAC
* * * * * *
29574625 ATAAATTTTAAAATAAAAAGTGTAAAAAATAAAAAAAATTAATTAATTAATGAATATTTTAATAA
448 ATGAATTTT--TATAAAAAATATAAAAAAT--AAAAAATTAATTAATTAATAAATATTTAAATAA
* *
29574690 TTTCATCAAAAGTTAAATTTTTTGAATGTATTGATAAGAAGTTGGAGTGTAAATAA
509 TTTCATTAAAA-TTAAATTTTTTGAATGTATTGATAA-AAGTT-GAGTGCAAATAA
29574746 TATATTTCAT
Statistics
Matches: 1014, Mismatches: 111, Indels: 114
0.82 0.09 0.09
Matches are distributed among these distances:
588 4 0.00
589 65 0.06
590 9 0.01
591 16 0.02
592 33 0.03
593 8 0.01
594 104 0.10
595 61 0.06
596 1 0.00
606 2 0.00
608 2 0.00
609 3 0.00
611 1 0.00
613 1 0.00
616 2 0.00
617 3 0.00
618 1 0.00
619 1 0.00
621 61 0.06
622 168 0.17
623 61 0.06
624 31 0.03
625 185 0.18
626 188 0.19
627 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (613 bp):
AATGTGGGTTCCTTCTTTCGTTTTTTTCTTTTGTTTTTTTGCATAATGATAGTACCCAAGAAAAG
ATTGTTTTTTTTTTTAATGATACTGATTGCTTTCCAAGTTCCTCTCTTCATACCTCATTATTGTT
AATACTTAATTTTTTACTCAATATAATCCCAATTTAAAATACAAATTTAAAAAATTCAAAAACCA
TCTCCCACAATCATCTTTTCCTATTCCCAACCTAAAATCTAAAGGATTTTAAACCTCAATCTAAT
CAAATTCAAAGAAAATTTCAACCATTTAAGTTAAAAAACATAAAATTAAAGATAAATTATTTATT
TTTTTTATTTTTTATTTGACTTTGTATTTAATTTCATAAGATTAAGATTTCATGTCGAAATATTT
GGGTGCAATTAAAAACTTTTTAAAATAAATTTTAAAAAATTTTAAAAATTTTTGAACATGAATTT
TTATAAAAAATATAAAAAATAAAAAATTAATTAATTAATAAATATTTAAATAATTTCATTAAAAT
TAAATTTTTTGAATGTATTGATAAAAGTTGAGTGCAAATAACAACACTCTTTTTTTTAATCATTG
CTCAACGTCATTCCTTTAAATTATTACT
Found at i:29574614 original size:9 final size:10
Alignment explanation
Indices: 29574593--29574619 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29574583 TTTTAAAAAT
29574593 AAATTTTTAA
1 AAATTTTTAA
29574603 AAATTTTTAA
1 AAATTTTTAA
29574613 AAATTTT
1 AAATTTT
29574620 CGAACATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATTTTTAA
Found at i:29576868 original size:13 final size:13
Alignment explanation
Indices: 29576850--29576877 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29576840 GAACGAATGA
29576850 AAGAACTGCCTGG
1 AAGAACTGCCTGG
29576863 AAGAACTGCCTGG
1 AAGAACTGCCTGG
29576876 AA
1 AA
29576878 TTGAACTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.29, T:0.14
Consensus pattern (13 bp):
AAGAACTGCCTGG
Found at i:29579557 original size:14 final size:14
Alignment explanation
Indices: 29579538--29579566 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29579528 TTAGTCGGTG
29579538 CCCAAAGTGACTAC
1 CCCAAAGTGACTAC
29579552 CCCAAAGTGACTAC
1 CCCAAAGTGACTAC
29579566 C
1 C
29579567 GGAAGGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.14, T:0.14
Consensus pattern (14 bp):
CCCAAAGTGACTAC
Found at i:29584212 original size:2 final size:2
Alignment explanation
Indices: 29584207--29584245 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29584197 TGTGTGCGCG
29584207 TA TA 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 TA TA T
29584246 TTAATGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29584993 original size:20 final size:19
Alignment explanation
Indices: 29584952--29584990 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29584942 TTTTTATTAC
*
29584952 ATTTTTTAAGTTTTTAACA
1 ATTTTTTAAGTTTTTAAAA
* *
29584971 ATTTTTTTATTTTTTAAAA
1 ATTTTTTAAGTTTTTAAAA
29584990 A
1 A
29584991 ATTAAAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTTTTAAGTTTTTAAAA
Found at i:29587008 original size:17 final size:17
Alignment explanation
Indices: 29586983--29587024 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
29586973 ACCATAATAA
* *
29586983 CTTAAACTATCTCTGCT
1 CTTATACTATATCTGCT
*
29587000 CTTATACTATATCTGTT
1 CTTATACTATATCTGCT
29587017 CTTATACT
1 CTTATACT
29587025 GTCTGTATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (17 bp):
CTTATACTATATCTGCT
Found at i:29590262 original size:16 final size:16
Alignment explanation
Indices: 29590241--29590271 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29590231 AAAAATAATT
29590241 TTTTATTAATTTTAAA
1 TTTTATTAATTTTAAA
*
29590257 TTTTATTATTTTTAA
1 TTTTATTAATTTTAA
29590272 TAATAACCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATTAATTTTAAA
Found at i:29590494 original size:14 final size:16
Alignment explanation
Indices: 29590475--29590509 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
29590465 TTTCACTTAT
29590475 AAAAAATTT-GA-AAA
1 AAAAAATTTAGAGAAA
29590489 AAAAAATTTAGAGAAA
1 AAAAAATTTAGAGAAA
29590505 AAAAA
1 AAAAA
29590510 GATGCATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 2 0.11
16 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (16 bp):
AAAAAATTTAGAGAAA
Found at i:29593955 original size:23 final size:22
Alignment explanation
Indices: 29593903--29593955 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
29593893 ATACTCAATC
*
29593903 TATAAAATTTTATCAATTTTAA
1 TATAAAACTTTATCAATTTTAA
*
29593925 TTTAAAAACTTTAT-AATTTTATCA
1 TAT-AAAACTTTATCAATTTTA--A
29593949 TATAAAA
1 TATAAAA
29593956 AATATGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 9 0.36
23 13 0.52
24 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAAAACTTTATCAATTTTAA
Found at i:29594777 original size:18 final size:18
Alignment explanation
Indices: 29594754--29594801 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
29594744 TAACTTACAA
29594754 ATTTAATCTAATTTTTA-T
1 ATTTAAT-TAATTTTTATT
*
29594772 ATTTAAATATATTTTTATT
1 ATTTAATTA-ATTTTTATT
29594791 ATTTAATTAAT
1 ATTTAATTAAT
29594802 AAAATATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 2 0.08
18 15 0.58
19 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATTAATTTTTATT
Found at i:29600212 original size:3 final size:3
Alignment explanation
Indices: 29600206--29600255 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
29600196 ATAATAATAA
* * * *
29600206 TAT TAT TAT TAT TAT TCTT TGT TAC TAT TAT TAT TAT TAT TAT AAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29600252 TAT T
1 TAT T
29600256 CTTTGGGGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29604333 original size:15 final size:15
Alignment explanation
Indices: 29604309--29604342 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29604299 AAAATGTTGT
*
29604309 TATT-AATAATATTA
1 TATTAAATAATATAA
29604323 TATTAAATAATATAA
1 TATTAAATAATATAA
29604338 TATTA
1 TATTA
29604343 TTTTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAATAATATAA
Found at i:29607484 original size:56 final size:56
Alignment explanation
Indices: 29607423--29607533 Score: 168
Period size: 56 Copynumber: 2.0 Consensus size: 56
29607413 TATAGAAATG
* * * *
29607423 GGGTGTATAACATTAAATGGGGTGCATTTAGAATTTCTCGATAAATAATATTTATT
1 GGGTGTATAACATTAAATGGGGAGAATTTAGAATTCCCCGATAAATAATATTTATT
* *
29607479 GGGTGTATAGCATTAAATGGGGAGAATTTAGAATTCCCCTATAAATAATATTTAT
1 GGGTGTATAACATTAAATGGGGAGAATTTAGAATTCCCCGATAAATAATATTTAT
29607534 AGCATACTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (56 bp):
GGGTGTATAACATTAAATGGGGAGAATTTAGAATTCCCCGATAAATAATATTTATT
Found at i:29608022 original size:21 final size:23
Alignment explanation
Indices: 29607979--29608024 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
29607969 GTAACAAGTT
29607979 TTTAATATTTTAGATTATCAAAA
1 TTTAATATTTTAGATTATCAAAA
*
29608002 TTTAA-ATTTTA-ATTATTAAAA
1 TTTAATATTTTAGATTATCAAAA
29608023 TT
1 TT
29608025 GAAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 6 0.27
23 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAATATTTTAGATTATCAAAA
Found at i:29610401 original size:48 final size:48
Alignment explanation
Indices: 29610333--29610431 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 48
29610323 TTTAATAAGC
*
29610333 AAGTTTAACTTGCAGAAGAAGAATTCTAAGAGAAAAATGATTCTTAAT
1 AAGTTTAACTTACAGAAGAAGAATTCTAAGAGAAAAATGATTCTTAAT
* * * * *
29610381 AAGTTTGACTTACAGGAGAAGAATTTTAAGAGGAAAGTGATTCTTAAT
1 AAGTTTAACTTACAGAAGAAGAATTCTAAGAGAAAAATGATTCTTAAT
29610429 AAG
1 AAG
29610432 CAAGTTTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (48 bp):
AAGTTTAACTTACAGAAGAAGAATTCTAAGAGAAAAATGATTCTTAAT
Found at i:29611132 original size:142 final size:142
Alignment explanation
Indices: 29610858--29611133 Score: 329
Period size: 142 Copynumber: 1.9 Consensus size: 142
29610848 TTTTTTGTGA
* * * ** ** *
29610858 GTTTGATTAATTATTTAATTTTACTTTCGTTGGTGTGATTGGATTTGCTTCTGTTGGTGTGATGG
1 GTTTGATTAATTATTTAATTTTACTTTCATTAGTGTGATTAGATTCACTTCTGTTAATGTGATGA
* * ** * * * * * *
29610923 ATTGAGGCTTTTTGACCTAATAAGTGGTATCAAAGCTATGATGATCCCTAATAGTGGTTGAGAGA
66 ATTGAGGCCTTTTGACCTAACAAGTGAAATCAAAACTATGACGATCCCCAACAATGATTGAGAGA
29610988 TATTCAATTTAG
131 TATTCAATTTAG
* * *
29611000 GTTTGATTAATTGTTTGATTTTACTTTCATTAGTGTGATTAGATTCATTTCTGTTAATGTGATGA
1 GTTTGATTAATTATTTAATTTTACTTTCATTAGTGTGATTAGATTCACTTCTGTTAATGTGATGA
* *
29611065 ATTGAGGCCTTTTGACTTAACAAGTGAAATTAAAACTATGACGATCCCCAACAATGATTGA-AGG
66 ATTGAGGCCTTTTGACCTAACAAGTGAAATCAAAACTATGACGATCCCCAACAATGATTGAGA-G
29611129 ATATT
130 ATATT
29611134 TGATTTGGAT
Statistics
Matches: 110, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
141 1 0.01
142 109 0.99
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (142 bp):
GTTTGATTAATTATTTAATTTTACTTTCATTAGTGTGATTAGATTCACTTCTGTTAATGTGATGA
ATTGAGGCCTTTTGACCTAACAAGTGAAATCAAAACTATGACGATCCCCAACAATGATTGAGAGA
TATTCAATTTAG
Found at i:29614825 original size:37 final size:42
Alignment explanation
Indices: 29614784--29614860 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
29614774 TTTGATTCAT
29614784 ATTTG-TTAAA-AA-AAATTATTT-TA-TTCATTTGTGTTCG
1 ATTTGTTTAAATAATAAATTATTTGTATTTCATTTGTGTTCG
*
29614821 ATTTGTTTAAATAATAAATTATTTGTATTTGATTTGTGTT
1 ATTTGTTTAAATAATAAATTATTTGTATTTCATTTGTGTT
29614861 TAATTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 5 0.15
38 5 0.15
39 2 0.06
40 9 0.26
41 2 0.06
42 11 0.32
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.55
Consensus pattern (42 bp):
ATTTGTTTAAATAATAAATTATTTGTATTTCATTTGTGTTCG
Found at i:29614900 original size:23 final size:23
Alignment explanation
Indices: 29614874--29614935 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
29614864 TTTAATTAAG
**
29614874 TTAAATGAATTTATTCATGAATA
1 TTAAATGAACATATTCATGAATA
29614897 TTAAATGAACATATTCATGAACATA
1 TTAAATGAACATATTCATG-A-ATA
*
29614922 TATAAATAAACATA
1 T-TAAATGAACATA
29614936 ATTATAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.52
24 1 0.03
25 4 0.12
26 11 0.33
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (23 bp):
TTAAATGAACATATTCATGAATA
Found at i:29614934 original size:26 final size:23
Alignment explanation
Indices: 29614885--29614935 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 23
29614875 TAAATGAATT
*
29614885 TATTCATGAATATTAAATGAACA
1 TATTCATGAATATTAAATAAACA
29614908 TATTCATGAACATATATAAATAAACA
1 TATTCATG-A-ATAT-TAAATAAACA
29614934 TA
1 TA
29614936 ATTATAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 4 0.17
26 11 0.46
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (23 bp):
TATTCATGAATATTAAATAAACA
Found at i:29614945 original size:26 final size:27
Alignment explanation
Indices: 29614893--29614955 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
29614883 TTTATTCATG
* *
29614893 AATAT-TAAATGAACATATTCATGAAC
1 AATATATAAATAAACATATTCATAAAC
29614919 -ATATATAAATAAACATAATT-ATAAAC
1 AATATATAAATAAACAT-ATTCATAAAC
*
29614945 AATAAATAAAT
1 AATATATAAAT
29614956 TATAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 15 0.48
27 12 0.39
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (27 bp):
AATATATAAATAAACATATTCATAAAC
Found at i:29614956 original size:18 final size:19
Alignment explanation
Indices: 29614925--29614970 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
29614915 GAACATATAT
*
29614925 AAATAAACATAATTATAAAC
1 AAATAAATA-AATTATAAAC
*
29614945 -AATAAATAAATTATAACC
1 AAATAAATAAATTATAAAC
29614963 AAATAAAT
1 AAATAAAT
29614971 TTAAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAATAAATTATAAAC
Found at i:29614967 original size:19 final size:20
Alignment explanation
Indices: 29614925--29614985 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 20
29614915 GAACATATAT
*
29614925 AAATAAACATAATTATAAAC
1 AAATAAATATAATTATAAAC
*
29614945 -AATAAATA-AATTATAACC
1 AAATAAATATAATTATAAAC
*
29614963 AAATAAATTTAA--ATAAAC
1 AAATAAATATAATTATAAAC
29614981 AAATA
1 AAATA
29614986 TAAACGAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 19 0.54
19 14 0.40
20 2 0.06
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAATATAATTATAAAC
Found at i:29628577 original size:26 final size:26
Alignment explanation
Indices: 29628541--29628597 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
29628531 TTCATTAATT
29628541 TTTTTTTTCAATCATAACTATAATAA
1 TTTTTTTTCAATCATAACTATAATAA
** *
29628567 TTTTTTTTCAATTGTAGCTATAATAA
1 TTTTTTTTCAATCATAACTATAATAA
29628593 TTTTT
1 TTTTT
29628598 GTTTTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.56
Consensus pattern (26 bp):
TTTTTTTTCAATCATAACTATAATAA
Found at i:29630754 original size:24 final size:24
Alignment explanation
Indices: 29630721--29630768 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29630711 ATTATTATGT
*
29630721 TAACACGTACA-AATGATATGTTTA
1 TAACAAGTACATAATGATAT-TTTA
*
29630745 TAACAAGTACATAATTATATTTTA
1 TAACAAGTACATAATGATATTTTA
29630769 ATATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (24 bp):
TAACAAGTACATAATGATATTTTA
Found at i:29632232 original size:17 final size:17
Alignment explanation
Indices: 29632212--29632244 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29632202 ATTTAATATA
29632212 TCATTATTTTT-ATTTTT
1 TCATT-TTTTTCATTTTT
29632229 TCATTTTTTTCATTTT
1 TCATTTTTTTCATTTT
29632245 GATTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TCATTTTTTTCATTTTT
Found at i:29632352 original size:20 final size:22
Alignment explanation
Indices: 29632313--29632353 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
29632303 TATTATACAA
29632313 TAAATAAATAGTATAAAAATAT
1 TAAATAAATAGTATAAAAATAT
*
29632335 TAAA-AAATA-TATACAAATA
1 TAAATAAATAGTATAAAAATA
29632354 ATTTATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATAAATAGTATAAAAATAT
Found at i:29633020 original size:24 final size:23
Alignment explanation
Indices: 29632976--29633020 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
29632966 AAAACATAGT
**
29632976 AATATTTTATTTATTTTATAATA
1 AATATTTTATTTATTACATAATA
29632999 AATATATTTATTTATTACATAA
1 AATAT-TTTATTTATTACATAA
29633021 ACCAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTTATTTATTACATAATA
Found at i:29633230 original size:30 final size:30
Alignment explanation
Indices: 29633194--29633273 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
29633184 TGAAAATATA
*
29633194 AAATTTATAATATAAAATAATTATAATTTT
1 AAATTTATAATATAAAATAATTATAATTAT
*
29633224 AAATTTATAATATAAAACAATTATAATTAT
1 AAATTTATAATATAAAATAATTATAATTAT
29633254 -AATTTATAATATAAAATAAT
1 AAATTTATAATATAAAATAAT
29633274 CACTTTACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 19 0.40
30 28 0.60
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
AAATTTATAATATAAAATAATTATAATTAT
Found at i:29633860 original size:44 final size:44
Alignment explanation
Indices: 29633797--29633884 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
29633787 CGTGTACTGG
*
29633797 ACATAATAATCATAATAAAATAAATACGATATACGATAAATTAT
1 ACATAATAATCATAATAAAATAAACACGATATACGATAAATTAT
29633841 ACATAATAATCATAATAAAATAAACACGATATACGATAAATTAT
1 ACATAATAATCATAATAAAATAAACACGATATACGATAAATTAT
29633885 GAATTAAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (44 bp):
ACATAATAATCATAATAAAATAAACACGATATACGATAAATTAT
Found at i:29634091 original size:11 final size:11
Alignment explanation
Indices: 29634075--29634103 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
29634065 TTATTGAATT
29634075 AAATTTAAACA
1 AAATTTAAACA
29634086 AAATTTAAACA
1 AAATTTAAACA
29634097 AAATTTA
1 AAATTTA
29634104 CTTTAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATTTAAACA
Found at i:29636971 original size:35 final size:36
Alignment explanation
Indices: 29636925--29636997 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
29636915 TTGATGTATT
**
29636925 TAATATTATAAATTT-AAATTTTTATGGTATTGATG
1 TAATATTATAAATTTAAAATTTTTATGACATTGATG
29636960 TAATATTATAAATTTAAAATTTTTATGACATTGATG
1 TAATATTATAAATTTAAAATTTTTATGACATTGATG
29636996 TA
1 TA
29636998 CTGTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 15 0.43
36 20 0.57
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (36 bp):
TAATATTATAAATTTAAAATTTTTATGACATTGATG
Found at i:29637640 original size:15 final size:15
Alignment explanation
Indices: 29637620--29637652 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29637610 GAATCAAAAT
29637620 ATTAATTTTAATA-AA
1 ATTAA-TTTAATATAA
29637635 ATTAATTTAATATAA
1 ATTAATTTAATATAA
29637650 ATT
1 ATT
29637653 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAATTTAATATAA
Found at i:29639478 original size:100 final size:100
Alignment explanation
Indices: 29639305--29639607 Score: 471
Period size: 100 Copynumber: 3.0 Consensus size: 100
29639295 CAAAGTAAGT
* * * * *
29639305 TTTCTTTCTGTTGGAACAGTATTGACAGATGAGATAGAAAGAGCGAGGCACGCTTGCGAGAATGG
1 TTTCTTTCTGTTGGAACAGTATTGACAGATGAGACAGAAAGAGCAAGACAGGCTTGCAAGAATGG
*
29639370 ATCCTGACTACCAGGAAAGGAAGGAATTAGCTGAG
66 ATCCTGACTACCAGGAAAGGAAGGAACTAGCTGAG
*
29639405 TTTCTTTCTGTTGGAACAGTATTGACAGATGAGACGGAAAGAGCAAGACAGGCTTGCAAGAATGG
1 TTTCTTTCTGTTGGAACAGTATTGACAGATGAGACAGAAAGAGCAAGACAGGCTTGCAAGAATGG
* *
29639470 ATCCTGACTACCAGGAAGGGAAGGAACTAGCTTAG
66 ATCCTGACTACCAGGAAAGGAAGGAACTAGCTGAG
* * *
29639505 TTTCTTTCTGTTGGTACAGTATCGACTGATGAGACAGAAAGAGCAAGACAGGCTTGCAAGAATGG
1 TTTCTTTCTGTTGGAACAGTATTGACAGATGAGACAGAAAGAGCAAGACAGGCTTGCAAGAATGG
* * *
29639570 ATGCTGATTACCAGAAAAGGAAGGAACTAGCTGAG
66 ATCCTGACTACCAGGAAAGGAAGGAACTAGCTGAG
29639605 TTT
1 TTT
29639608 AACACAAGAA
Statistics
Matches: 185, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 185 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (100 bp):
TTTCTTTCTGTTGGAACAGTATTGACAGATGAGACAGAAAGAGCAAGACAGGCTTGCAAGAATGG
ATCCTGACTACCAGGAAAGGAAGGAACTAGCTGAG
Found at i:29643261 original size:6 final size:6
Alignment explanation
Indices: 29643250--29643284 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
29643240 TTCTCCTGTT
29643250 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
29643285 TGTGTAGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:29647603 original size:15 final size:15
Alignment explanation
Indices: 29647579--29647608 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29647569 TTTTTCTGCA
29647579 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
29647594 AAAAAGAAAAAAAAA
1 AAAAA-AAAAAAAAA
29647609 ACCAACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:29647603 original size:16 final size:16
Alignment explanation
Indices: 29647578--29647609 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
29647568 GTTTTTCTGC
29647578 AAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
29647594 AAAAAGAAAAAAAAAA
1 AAAAA-AAAAAAAAAA
29647610 CCAACTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:29652754 original size:21 final size:22
Alignment explanation
Indices: 29652713--29652754 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29652703 TATTGGGCCT
29652713 GAAGTAATATACATAACAATACA
1 GAAGTAATATA-ATAACAATACA
*
29652736 GAAGTAATAT-ATTACAATA
1 GAAGTAATATAATAACAATA
29652755 AACCCATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (22 bp):
GAAGTAATATAATAACAATACA
Found at i:29653154 original size:22 final size:22
Alignment explanation
Indices: 29653126--29653172 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
29653116 TTTCTTCTCT
*
29653126 TTTTTC-TCTTTACTTTTCCTGG
1 TTTTTCTTCTTT-CTCTTCCTGG
*
29653148 TTTTTCTTCTTTCTCTTCTTGG
1 TTTTTCTTCTTTCTCTTCCTGG
29653170 TTT
1 TTT
29653173 GTGACACCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.02, C:0.21, G:0.09, T:0.68
Consensus pattern (22 bp):
TTTTTCTTCTTTCTCTTCCTGG
Found at i:29654440 original size:21 final size:21
Alignment explanation
Indices: 29654423--29654463 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
29654413 AAAAATATTT
29654423 TTAATTTATTATATAATAAAA
1 TTAATTTATTATATAATAAAA
29654444 TTAATTTATTATATAATAAA
1 TTAATTTATTATATAATAAA
29654464 TTTTAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTTATTATATAATAAAA
Done.