Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 11 of 93
Found at i:5546109 original size:9 final size:9
Alignment explanation
Indices: 5546070--5546119 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
5546060 NNNNNNNNNN
5546070 TTTTTATTT
1 TTTTTATTT
5546079 TATTTTATATAT
1 T-TTTTAT-T-T
5546091 TTTTTA--T
1 TTTTTATTT
5546098 TTTTTATTT
1 TTTTTATTT
5546107 TTTTTATTT
1 TTTTTATTT
5546116 TTTT
1 TTTT
5546120 ATCTAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.19
9 15 0.42
10 6 0.17
11 6 0.17
12 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5546117 original size:16 final size:16
Alignment explanation
Indices: 5546071--5546118 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
5546061 NNNNNNNNNT
*
5546071 TTTTATTTTATTTTATA
1 TTTT-TTTTATTTTTTA
*
5546088 TATTTTTTATTTTTTA
1 TTTTTTTTATTTTTTA
5546104 TTTTTTTTATTTTTT
1 TTTTTTTTATTTTTT
5546119 TATCTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTATTTTTTA
Found at i:5546118 original size:7 final size:7
Alignment explanation
Indices: 5546076--5546109 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
5546066 NNNNTTTTTA
5546076 TTTTATT
1 TTTTATT
5546083 TTATATATT
1 TT-T-TATT
5546092 TTTTATT
1 TTTTATT
5546099 TTTTATT
1 TTTTATT
5546106 TTTT
1 TTTT
5546110 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:5547040 original size:8 final size:8
Alignment explanation
Indices: 5547027--5547074 Score: 78
Period size: 8 Copynumber: 5.9 Consensus size: 8
5547017 CCATCCCGAT
5547027 TTTTTTTA
1 TTTTTTTA
5547035 TTTTTTTA
1 TTTTTTTA
5547043 TTTTTTTA
1 TTTTTTTA
5547051 TTTTATTTA
1 TTTT-TTTA
*
5547060 TTTATTTA
1 TTTTTTTA
5547068 TTTTTTT
1 TTTTTTT
5547075 TAATTTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 30 0.81
9 7 0.19
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:5547047 original size:17 final size:17
Alignment explanation
Indices: 5547027--5547076 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
5547017 CCATCCCGAT
5547027 TTTTTTTA-TTTTTTTA
1 TTTTTTTATTTTTTTTA
*
5547043 TTTTTTTATTTTATTTA
1 TTTTTTTATTTTTTTTA
*
5547060 TTTATTTATTTTTTTTA
1 TTTTTTTATTTTTTTTA
5547077 ATTTATGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTATTTTTTTTA
Found at i:5547059 original size:25 final size:25
Alignment explanation
Indices: 5547025--5547074 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
5547015 AGCCATCCCG
* *
5547025 ATTTTTTTTATTTTTTTATTTTTTT
1 ATTTTATTTATTTATTTATTTTTTT
5547050 ATTTTATTTATTTATTTATTTTTTT
1 ATTTTATTTATTTATTTATTTTTTT
5547075 TAATTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (25 bp):
ATTTTATTTATTTATTTATTTTTTT
Found at i:5547061 original size:4 final size:4
Alignment explanation
Indices: 5547031--5547082 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
5547021 CCCGATTTTT
* * *
5547031 TTTA TTTT TTTA TTTT TTTA TTTTA TTTA TTTA TTTA TTT- TTT- TTAA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5547078 TTTA T
1 TTTA T
5547083 GTGTCTACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 5 0.12
4 31 0.77
5 4 0.10
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTA
Found at i:5548758 original size:2 final size:2
Alignment explanation
Indices: 5548751--5548793 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5548741 TGAGATTTAC
5548751 TA TA TA TA TA TA TA TA T- TA TA TA TA -A TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5548790 TA TA
1 TA TA
5548794 ATTTCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5548773 original size:9 final size:9
Alignment explanation
Indices: 5548751--5548793 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
5548741 TGAGATTTAC
5548751 TATATATA-
1 TATATATAT
5548759 TATATATAT
1 TATATATAT
*
5548768 TATATATAA
1 TATATATAT
5548777 TATATATAT
1 TATATATAT
5548786 TATATATA
1 TATATATA
5548794 ATTTCTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TATATATAT
Found at i:5548781 original size:18 final size:18
Alignment explanation
Indices: 5548751--5548795 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
5548741 TGAGATTTAC
5548751 TATATAT-ATATATATAT
1 TATATATAATATATATAT
5548768 TATATATAATATATATAT
1 TATATATAATATATATAT
5548786 TATATATAAT
1 TATATATAAT
5548796 TTCTTCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATATAATATATATAT
Found at i:5568526 original size:2 final size:2
Alignment explanation
Indices: 5568519--5568552 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5568509 AGGAAATGGC
*
5568519 GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5568553 TGGAATGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5581107 original size:16 final size:16
Alignment explanation
Indices: 5581086--5581119 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5581076 AAAGATGAGT
*
5581086 CATGTCAACATTGTGC
1 CATGTCAACATTATGC
*
5581102 CATGTCAGCATTATGC
1 CATGTCAACATTATGC
5581118 CA
1 CA
5581120 CATCATCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (16 bp):
CATGTCAACATTATGC
Found at i:5595359 original size:3 final size:3
Alignment explanation
Indices: 5595351--5595385 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
5595341 AAATGTAATA
5595351 TAT TAT TAT TAT TAT TAT TAT TAT TAT TCAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT T
5595386 TAGGTACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5601063 original size:2 final size:2
Alignment explanation
Indices: 5601056--5601090 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5601046 CAGAATTGGT
5601056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5601091 TCAAGGAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5604912 original size:9 final size:9
Alignment explanation
Indices: 5604898--5604935 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5604888 ATCCCTGACT
5604898 CATGATTTC
1 CATGATTTC
5604907 CATGATTTC
1 CATGATTTC
*
5604916 CATGATTCC
1 CATGATTTC
*
5604925 CGTGA-TTC
1 CATGATTTC
5604933 CAT
1 CAT
5604936 TCACATTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (9 bp):
CATGATTTC
Found at i:5612950 original size:32 final size:32
Alignment explanation
Indices: 5612913--5612997 Score: 134
Period size: 32 Copynumber: 2.7 Consensus size: 32
5612903 CACATTTTGG
*
5612913 TGACGTGACAATGTCACGTGGTACCGACGTGA
1 TGACGTGACAATATCACGTGGTACCGACGTGA
* *
5612945 TGACGTAACAATATCACGTGGTATCGACGTGA
1 TGACGTGACAATATCACGTGGTACCGACGTGA
*
5612977 TGACGTGATAATATCACGTGG
1 TGACGTGACAATATCACGTGG
5612998 CATTAATATG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (32 bp):
TGACGTGACAATATCACGTGGTACCGACGTGA
Found at i:5613010 original size:32 final size:32
Alignment explanation
Indices: 5612913--5613011 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 32
5612903 CACATTTTGG
* * * * * *
5612913 TGACGTGACAATGTCACGTGGTACCGACGTGA
1 TGACGTAACAATATCACGTGGCATCAACATGA
* * *
5612945 TGACGTAACAATATCACGTGGTATCGACGTGA
1 TGACGTAACAATATCACGTGGCATCAACATGA
* * * *
5612977 TGACGTGATAATATCACGTGGCATTAATATGA
1 TGACGTAACAATATCACGTGGCATCAACATGA
5613009 TGA
1 TGA
5613012 TATAACATTG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (32 bp):
TGACGTAACAATATCACGTGGCATCAACATGA
Found at i:5613957 original size:59 final size:60
Alignment explanation
Indices: 5613864--5613985 Score: 212
Period size: 59 Copynumber: 2.0 Consensus size: 60
5613854 ATTTTGTTTA
5613864 ATATTTCATGTTATTTTTTTTAGGAAAAATTTTTTGGATTAAAGATTGCA-TTATGACTG
1 ATATTTCATGTTATTTTTTTTAGGAAAAATTTTTTGGATTAAAGATTGCATTTATGACTG
*
5613923 NATATTTCATGTTA-TTTTTTTAGGTAAAATTTTTTGGATTAAAGATTGCATTTATGACTG
1 -ATATTTCATGTTATTTTTTTTAGGAAAAATTTTTTGGATTAAAGATTGCATTTATGACTG
5613983 ATA
1 ATA
5613986 AAATTAAATA
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
59 38 0.63
60 22 0.37
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.49
Consensus pattern (60 bp):
ATATTTCATGTTATTTTTTTTAGGAAAAATTTTTTGGATTAAAGATTGCATTTATGACTG
Found at i:5617733 original size:2 final size:2
Alignment explanation
Indices: 5617726--5617843 Score: 125
Period size: 2 Copynumber: 60.0 Consensus size: 2
5617716 ACAGAAAACA
* * * *
5617726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT 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
*
5617768 AT AT AT AT AT AT AT A- AT NA- AC A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5617808 AT AT AT AT AT GT GT GT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5617844 CTAAATGTGA
Statistics
Matches: 108, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
1 3 0.03
2 104 0.96
3 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5617770 original size:32 final size:32
Alignment explanation
Indices: 5617729--5617852 Score: 160
Period size: 32 Copynumber: 3.9 Consensus size: 32
5617719 GAAAACAATA
5617729 TATATATATATATATATATATATATGTGTGTG
1 TATATATATATATATATATATATATGTGTGTG
***** *
5617761 TATATATATATATATATATATA-ATNAACAATA
1 TATATATATATATATATATATATAT-GTGTGTG
5617793 TATATATATATATATATATATATATGTGTGTG
1 TATATATATATATATATATATATATGTGTGTG
* *
5617825 TATATATATATATATATATCTAAATGTG
1 TATATATATATATATATATATATATGTG
5617853 AATGGTCTTC
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
31 2 0.03
32 72 0.95
33 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (32 bp):
TATATATATATATATATATATATATGTGTGTG
Found at i:5617823 original size:64 final size:63
Alignment explanation
Indices: 5617722--5617843 Score: 235
Period size: 64 Copynumber: 1.9 Consensus size: 63
5617712 TAAGACAGAA
5617722 AACAATATATATATATATATATATATATATATGTGTGTGTATATATATATATATATATATAAT
1 AACAATATATATATATATATATATATATATATGTGTGTGTATATATATATATATATATATAAT
5617785 NAACAATATATATATATATATATATATATATATGTGTGTGTATATATATATATATATAT
1 -AACAATATATATATATATATATATATATATATGTGTGTGTATATATATATATATATAT
5617844 CTAAATGTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (63 bp):
AACAATATATATATATATATATATATATATATGTGTGTGTATATATATATATATATATATAAT
Found at i:5625337 original size:2 final size:2
Alignment explanation
Indices: 5625330--5625371 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5625320 AGCANAATAA
5625330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5625372 GGCCTAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5641638 original size:18 final size:19
Alignment explanation
Indices: 5641605--5641643 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5641595 ATTATTGTTG
5641605 ATATAAAATTAAATT-ATA
1 ATATAAAATTAAATTAATA
**
5641623 ATATAAAATTTTATTAATA
1 ATATAAAATTAAATTAATA
5641642 AT
1 AT
5641644 TTTAAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAAAATTAAATTAATA
Found at i:5641742 original size:131 final size:130
Alignment explanation
Indices: 5641607--5641855 Score: 283
Period size: 131 Copynumber: 1.9 Consensus size: 130
5641597 TATTGTTGAT
**
5641607 ATAAAATTAAATT-ATAATATAAAATTTTATTAATAA-TTTTA-AATTCATTAATATAAATAGAT
1 ATAAAATTAAATTAATAAT-TAAAA-TTTA-T-ATAAGTTTTATAATT-ACCAATATAAATAGA-
* * * * *
5641669 CA-AAA-ATAAAAAAATTAATATTAGATTTTTACATTAAATATCGTCATAAATATAAAATTAAAT
60 CATAAATAGAAAAAAACTAACATTAGATTTTTACACTAAATATCGTAATAAATATAAAATTAAAT
5641732 CATAAC
125 CATAAC
** * *
5641738 ATAAAATTTTATTAATAATTTAAATTTATATAAGTTTTTATAATTACCAATATAAATGGACATAA
1 ATAAAATTAAATTAATAATTAAAATTTATATAAG-TTTTATAATTACCAATATAAATAGACATAA
* *
5641803 ATAGAAAAAAACTAACATTAGATTTTTACACTAACTATCGTAATAGATATAAA
65 ATAGAAAAAAACTAACATTAGATTTTTACACTAAATATCGTAATAAATATAAA
5641856 GTAAAAAAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
128 4 0.04
129 3 0.03
130 24 0.24
131 63 0.64
132 5 0.05
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (130 bp):
ATAAAATTAAATTAATAATTAAAATTTATATAAGTTTTATAATTACCAATATAAATAGACATAAA
TAGAAAAAAACTAACATTAGATTTTTACACTAAATATCGTAATAAATATAAAATTAAATCATAAC
Found at i:5659662 original size:2 final size:2
Alignment explanation
Indices: 5659655--5659708 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
5659645 TTGATAATTG
* * *
5659655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5659697 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5659709 TCAAAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5662836 original size:6 final size:6
Alignment explanation
Indices: 5662825--5662851 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5662815 AATGAGGTCC
5662825 TGTATT TGTATT TGTATT TGTATT TGT
1 TGTATT TGTATT TGTATT TGTATT TGT
5662852 GAATTAGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.19, T:0.67
Consensus pattern (6 bp):
TGTATT
Found at i:5663176 original size:31 final size:31
Alignment explanation
Indices: 5663141--5663203 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
5663131 TAAAATACTT
*
5663141 ACACGTACACGTTTAAT-ACACGTGTAACACG
1 ACACG-ACACGATTAATAACACGTGTAACACG
*
5663172 ACACGACACGATTAATAACACGTTTAACACG
1 ACACGACACGATTAATAACACGTGTAACACG
5663203 A
1 A
5663204 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (31 bp):
ACACGACACGATTAATAACACGTGTAACACG
Found at i:5663285 original size:15 final size:14
Alignment explanation
Indices: 5663258--5663295 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
5663248 TTTAAAATTT
5663258 ATAATTAT-AAAAA
1 ATAATTATAAAAAA
5663271 ATAATTATAATAAAA
1 ATAATTATAA-AAAA
*
5663286 ATAATAATAA
1 ATAATTATAA
5663296 CATCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATTATAAAAAA
Found at i:5663508 original size:18 final size:18
Alignment explanation
Indices: 5663465--5663510 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5663455 TGTCACGTAT
*
5663465 ACACGTTTAAACACGATA
1 ACACGATTAAACACGATA
* * *
5663483 ATATGATTACACACGATA
1 ACACGATTAAACACGATA
5663501 ACACGATTAA
1 ACACGATTAA
5663511 GTAAACGTGT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.24
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:5674703 original size:19 final size:19
Alignment explanation
Indices: 5674675--5674711 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5674665 ACATGTATTA
5674675 ATATTATATTAATTAATGG
1 ATATTATATTAATTAATGG
* *
5674694 ATATTTTATTTATTAATG
1 ATATTATATTAATTAATG
5674712 ACATATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
ATATTATATTAATTAATGG
Found at i:5675034 original size:2 final size:2
Alignment explanation
Indices: 5675029--5675072 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
5675019 AAAAAAGATC
5675029 AT AT AT CAT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5675071 AT
1 AT
5675073 GAAACAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5708621 original size:27 final size:27
Alignment explanation
Indices: 5708527--5708623 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 27
5708517 TGGATGACAA
* * * * *
5708527 GATAAAATATAACATAAAATATAATAT
1 GATAAAAAATAATATAAAAAATGATGT
* * * *
5708554 TATAAAAAATTATATAAAAAGTGACGT
1 GATAAAAAATAATATAAAAAATGATGT
* * * *
5708581 AATGAAACACAATATAAAAAATGATGT
1 GATAAAAAATAATATAAAAAATGATGT
5708608 GATAAAAAATAATATA
1 GATAAAAAATAATATA
5708624 TTAAAATTCT
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (27 bp):
GATAAAAAATAATATAAAAAATGATGT
Found at i:5709273 original size:15 final size:16
Alignment explanation
Indices: 5709253--5709285 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5709243 TTTTATTATT
*
5709253 TTTATAAA-ATAATTA
1 TTTATAAATATAAATA
5709268 TTTATAAATATAAATA
1 TTTATAAATATAAATA
5709284 TT
1 TT
5709286 AAATCAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATAAATATAAATA
Found at i:5719340 original size:41 final size:41
Alignment explanation
Indices: 5719283--5719365 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
5719273 CCACCTCACC
*
5719283 TGACATTCTTCATTTATAAACGCATAAATACACAAGGAGCA
1 TGACATTCTTCATTTATAAACGCATAAACACACAAGGAGCA
* *
5719324 TGACATTCTTCATTTATATATGCATAAACACACAAGGAGCA
1 TGACATTCTTCATTTATAAACGCATAAACACACAAGGAGCA
5719365 T
1 T
5719366 CAATATCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (41 bp):
TGACATTCTTCATTTATAAACGCATAAACACACAAGGAGCA
Found at i:5721770 original size:23 final size:24
Alignment explanation
Indices: 5721721--5721771 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5721711 TCCTTAATTG
* * *
5721721 TTTTTAAAATTTATATAATAATAA
1 TTTTTAAAATTAATAAAAAAATAA
*
5721745 TTTTTTAAATTAATAAAAAAAT-A
1 TTTTTAAAATTAATAAAAAAATAA
5721768 TTTT
1 TTTT
5721772 AATCATTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTTAAAATTAATAAAAAAATAA
Found at i:5722815 original size:21 final size:20
Alignment explanation
Indices: 5722774--5722829 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5722764 TTTAACATTA
5722774 TTTATTTATTAAA-T-AAATT
1 TTTATTTA-TAAATTAAAATT
*
5722793 TTT-TTAATAAAATTAAAATT
1 TTTATTTAT-AAATTAAAATT
5722813 TTTATTTATAAATTAAA
1 TTTATTTATAAATTAAA
5722830 TAAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 1 0.03
18 6 0.19
19 4 0.13
20 16 0.52
21 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATTTATAAATTAAAATT
Found at i:5726097 original size:19 final size:19
Alignment explanation
Indices: 5726073--5726109 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5726063 CTTCTTAACT
5726073 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
*
5726092 TCAAATCATACTCTAATA
1 TCAAATCATACTCCAATA
5726110 AGTCAAATGG
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:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:5735976 original size:17 final size:16
Alignment explanation
Indices: 5735934--5735976 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5735924 GCATATGAAA
*
5735934 ATTTATTTAGTATTTT
1 ATTTATTTAGGATTTT
*
5735950 AGTTAGTTTAGGATTTT
1 ATTTA-TTTAGGATTTT
5735967 ATTTTATTTA
1 A-TTTATTTA
5735977 TTTAGTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (16 bp):
ATTTATTTAGGATTTT
Found at i:5743671 original size:54 final size:54
Alignment explanation
Indices: 5743525--5743804 Score: 281
Period size: 54 Copynumber: 5.2 Consensus size: 54
5743515 AATATCGAAG
* * * * * * * * *
5743525 TGGAGTATGAGGACCCGAAGCCCCAGGTGGAGAATGAGGGTCCAAAGTCTGAGG
1 TGGAGAATGATGATCCGAAGCCCCAGCTGGAGAATGTGGGTTCAAAGCCTCAGC
*** ** * * *
5743579 TGGAGAATGATGATTTAAAGTACCAGCTAGAGAGTGTGGGTTCAAAGTCTCAGC
1 TGGAGAATGATGATCCGAAGCCCCAGCTGGAGAATGTGGGTTCAAAGCCTCAGC
** * ** *
5743633 TGGAGAATGAAAATCTGAAGCCCCAGAGGGAGAATGTGGGTTCAAAGGCTCAGC
1 TGGAGAATGATGATCCGAAGCCCCAGCTGGAGAATGTGGGTTCAAAGCCTCAGC
* * *
5743687 TGGAGAATGATGATCCAAAGCCCCAGCTGGAGAGTGTGGGTTCAAAGCCTCTGC
1 TGGAGAATGATGATCCGAAGCCCCAGCTGGAGAATGTGGGTTCAAAGCCTCAGC
* * * * *
5743741 TGGAGAATGATGATCCGAAGCCCCAGCTGGACATTGAGGATTCAAAGCCCCAGC
1 TGGAGAATGATGATCCGAAGCCCCAGCTGGAGAATGTGGGTTCAAAGCCTCAGC
5743795 TGGAGAATGA
1 TGGAGAATGA
5743805 GGGTTTGAAG
Statistics
Matches: 184, Mismatches: 42, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 184 1.00
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (54 bp):
TGGAGAATGATGATCCGAAGCCCCAGCTGGAGAATGTGGGTTCAAAGCCTCAGC
Found at i:5743691 original size:27 final size:27
Alignment explanation
Indices: 5743602--5743809 Score: 125
Period size: 27 Copynumber: 7.7 Consensus size: 27
5743592 TTTAAAGTAC
* * *
5743602 CAGCTAGAGAGTGTGGGTTCAAAGTCT
1 CAGCTGGAGAATGTGGGTTCAAAGCCT
**** * *
5743629 CAGCTGGAGAATG-AAAATCTGAAGCCC
1 CAGCTGGAGAATGTGGGTTC-AAAGCCT
** *
5743656 CAGAGGGAGAATGTGGGTTCAAAGGCT
1 CAGCTGGAGAATGTGGGTTCAAAGCCT
* * *
5743683 CAGCTGGAGAATGAT-GATCCAAAGCCC
1 CAGCTGGAGAATG-TGGGTTCAAAGCCT
*
5743710 CAGCTGGAGAGTGTGGGTTCAAAGCCT
1 CAGCTGGAGAATGTGGGTTCAAAGCCT
* * * * *
5743737 CTGCTGGAGAATGAT-GATCCGAAGCCC
1 CAGCTGGAGAATG-TGGGTTCAAAGCCT
* * * * *
5743764 CAGCTGGACATTGAGGATTCAAAGCCC
1 CAGCTGGAGAATGTGGGTTCAAAGCCT
*
5743791 CAGCTGGAGAATGAGGGTT
1 CAGCTGGAGAATGTGGGTT
5743810 TGAAGGCTCC
Statistics
Matches: 132, Mismatches: 43, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
26 3 0.02
27 125 0.95
28 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.19
Consensus pattern (27 bp):
CAGCTGGAGAATGTGGGTTCAAAGCCT
Found at i:5743714 original size:108 final size:107
Alignment explanation
Indices: 5743539--5743804 Score: 316
Period size: 108 Copynumber: 2.5 Consensus size: 107
5743529 GTATGAGGAC
* * * * ** *
5743539 CCGAAGCCCCAGGTGGAGAATGAGGGTCCAAAGTCTGAGGTGGAGAATGATGATTTAAAGTACCA
1 CCGAAGCCCCAGG-GGAGAATGAGGGTTCAAAGCCTCAGCTGGAGAATGATGATCCAAAGCACCA
*
5743604 GCTAGAGAGTGTGGGTTCAAAGTCTCAGCTGGAGAATGAAAAT
65 GCTAGAGAGTGTGGGTTCAAAGCCTCAGCTGGAGAATGAAAAT
* * * *
5743647 CTGAAGCCCCAGAGGGAGAATGTGGGTTCAAAGGCTCAGCTGGAGAATGATGATCCAAAGCCCCA
1 CCGAAGCCCCAG-GGGAGAATGAGGGTTCAAAGCCTCAGCTGGAGAATGATGATCCAAAGCACCA
* * **
5743712 GCTGGAGAGTGTGGGTTCAAAGCCTCTGCTGGAGAATGATGAT
65 GCTAGAGAGTGTGGGTTCAAAGCCTCAGCTGGAGAATGAAAAT
* * * * *
5743755 CCGAAGCCCCAGCTGGACATTGAGGATTCAAAGCCCCAGCTGGAGAATGA
1 CCGAAGCCCCAG-GGGAGAATGAGGGTTCAAAGCCTCAGCTGGAGAATGA
5743805 GGGTTTGAAG
Statistics
Matches: 133, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
108 132 0.99
109 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (107 bp):
CCGAAGCCCCAGGGGAGAATGAGGGTTCAAAGCCTCAGCTGGAGAATGATGATCCAAAGCACCAG
CTAGAGAGTGTGGGTTCAAAGCCTCAGCTGGAGAATGAAAAT
Found at i:5750944 original size:226 final size:225
Alignment explanation
Indices: 5750451--5754688 Score: 4981
Period size: 226 Copynumber: 19.0 Consensus size: 225
5750441 TGAGTGGCTA
* * *
5750451 ACCTAAGGTGAGAGCCACTTTGTGGTGCTTAGGGAAATAAACAAACTTTGAAGTGTGGCCATGTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGG-CATGTA
* * * * *
5750516 CATTAAGGAATGATGTTGCCGATATGTGAATCTAACATCAGGAATTTGGTGCATTCTTATTGA-A
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATT-ATA
5750580 CAATTGAAGGTATAATGGTGCAAAACTAATATTTC----A-TA-ACAAGGCATTCCTATTGTGTA
129 CAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTA
* *
5750639 ATAAAGACACAATAGTGCTTATGTGAACATAT
194 ATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * *
5750671 TCCTAAGGTGAGAGCCACATTGTGGTGCTTAGAGAAATAAACAAACTTTGAGATGTGGCAATGTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGGC-ATGTA
* * * * *
5750736 CATTAGGGAATAATGTTGCCAATATGTGAATCTAGCATCGGGTACTTGATGCATTCCTCTTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
5750801 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
5750866 TAAAGGCACAATGGTGCTTATGTGAACATAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * *
5750897 ACCTAAGGTAAGAACCACTTTGTCGTGCTTAGAGAAATAAACAAACTTTGAGGTGCAGGCATATG
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTG-TGGC--ATG
5750962 TACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGG-AGTTTGGTGCATTCCTATTA
63 TACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTA-TTTGGTGCATTCCTATTA
* * * * *
5751026 CACAATTGAAGGTATAATGGTGCAAAACAAATATTTCATCTATTAGACAATGCATTTCTATTGTG
127 TACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTG
* * * **
5751091 TAATAAAGGCATAGTGGTGTTTATACGAACATAT
192 TAATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * *
5751125 ACCTAAGGTGAGAGCCACTTTATGATGCTTAGAGAAATAAGCAAACTTTGAGGTGTGGGCATGTG
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GGCATGTA
* *
5751190 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACGTTGGGTATTTGGTGCATTCCTATTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
*
5751255 AATTGAAGGTACAATGGT-----AC----ATTTC---TATTATG-CAAGGCATTCCTATTGTGTA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTA-GACAAGGCATTCCTATTGTGTA
*
5751307 ATAAA-GCAAAAATGGTG-TTAATGTGAACATAT
194 ATAAAGGC-ACAATGGTGCTT-ATGTGAACATAT
* *
5751339 ACTTAAGGTCA-AAGCCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGGGCATGT
1 ACCTAAGGTGAGAA-CCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GGCATGT
* *
5751403 ACATTAAGGTATAATGTTGCCGATA--TG--------A-C-GGTATTTGGTGCATTCCTATTATA
64 ACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATA
* * * ** *
5751456 CAATTTAAGGTATAATGGTGCAAAATTAATATTTCATCTATTAGATGAGGCATTCCTATTCTGTA
129 CAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTA
* * *
5751521 ATAAAGGCACAGTGGTGCTCATGTAAACATAT
194 ATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * * *
5751553 ACATAAGGTGAGAACCAGTTTGTGGTGTTTAGAAAAATAAACAAACTTAGAGGTGTGGGCATGCA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GGCATGTA
* *
5751618 TATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
* *
5751683 AATTGAAGGTATAATGGTGCCAAACTAATATTTCATATATTAGACAAGGCGTTCCTATTGTGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
* *
5751748 TAAAGGCACAATGGTGCTCATGTAAACATAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * *
5751779 ACATAAGGTGAGAACCAGTTTGTGGTGTTTAGAAAAATAAACAAACTTAGAGGTGTGGGCATGTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GGCATGTA
* *
5751844 TATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
* *
5751909 AATTGAAGGTATAATGGTGCCAAACTAATATTTCATATATTAGACAAGGCGTTCCTATTGTGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
*
5751974 TAAAGGCACAATGGTGCTTATGTCAACATAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * * * * * *
5752005 GCATAAGGTGTGAACTACTTTGTGGTGCATATAAAAATAAACAAACTTTGAGGTGAGGGCATCTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTG-TGGCATGTA
* * *** *
5752070 CATTAAGGAATAATATTGGCAATATGTGAATCTAACATAACGTATTTGGTGCCTTCCTATTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
* **
5752135 AATTGAAGGTATAATGGTACAAAACTAATATTTCATATATTAGACAAGGCATTTTTATTGTGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
* * *
5752200 TAAAGGTACAATGGTGCTTATATGAACAGAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * * *
5752231 ACTTAAGGTAAGAACCACTTTGTGGTGTTTAGAGAAATAAACAAACTTTGAGGTGTGGGTATATG
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GG--CATG
* * *
5752296 TACATTAAGGAATAATGTTGCCGATATGTGAATCTAA-ACTCGAGTATTTGATGCATTCCTA-T-
63 TACATTAAGGAATAATGTTGCCAATATGTGAATCTAACA-TCGGGTATTTGGTGCATTCCTATTA
* * * * * * * *
5752358 T---A-TGCA---A-AATGGTGCAAAATTAATATTTAATGTATTAGAGAAGGCGTTCCTATTATA
127 TACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTG
* * * *
5752415 TACTAAAGGGACAATGGTGCTAACT-TGAATATAT
192 TAATAAAGGCACAATGGTGCTTA-TGTGAACATAT
* * * *
5752449 ACCTAAGAT-ATGAACCACTTTGTGGTGATTAGAGAATTAAACAAACTTTGAGGTGCGG---G--
1 ACCTAAGGTGA-GAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGGCATGTA
* * *
5752508 CA-T---GTAT-AT-TTGCCAATGTGTGAATCTAACATTGGGTATTTGGTGCATTCCTATTATAT
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCC-----TAT
* *
5752567 TATACAATTGAAGGTATAATGGTGTAAAACTAATATTTCATATATTAGACAAGACATTCCTATTG
125 TATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTG
5752632 TGTAATAAAGGCACAATGGTGCTTATGTGAACATAT
190 TGTAATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * *
5752668 ACTTAA-GTGATAGCCACTTTGTGGTTGTGGTCTTTGGAGAAATAAAC-AACTTTTGCGGTGTGG
1 ACCTAAGGTGAGAACCACTTTGT-G--GT-G-C-TTAGAGAAATAAACAAAC-TTTGAGGTGT-G
*
5752731 GCATGTACATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCT
58 GCATGTACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCT
*
5752796 ATTATACAATTGAAGGTATAATGGTGCAAAACTAGTATTTCATATATTAGACATA-GCATTCCTA
123 ATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACA-AGGCATTCCTA
* ** *
5752860 TTGTGTAATAAGGGTGCAATGGTGCTTATATGAACATAT
187 TTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATAT
** * *
5752899 ATTTAAGATGAGAACCACTTTGTGGTGTTTAGAGAAATAAACAAACTTTGAGGTGTAGGCATGTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GGCATGTA
* * * * * ** * *
5752964 TATTAA-AACATAATGTTTCCAACATGTGAATCAAACATTTGGTGTTTAGTGCATTCCTATTATA
65 CATTAAGGA-ATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATA
* ** *
5753028 CAATTGAAGGTGTAATGGTTTAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTA
129 CAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTA
* * * *
5753093 ACAAAGGCACAATGGCGTTTATGTGAGCATAT
194 ATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * * *
5753125 ACCTAAGGTAAGAACTACTTTATGGTGCTTAGAGAAATAAACAAACATTGAGGTGAGAGCATCTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTG-GCATGTA
* * * **
5753190 CATTAACGTATAATGTTGCCGATATGTGAATCTAATGTCGGGTATTTGGTGCATTCCTATTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
5753255 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
* *
5753320 CAAAGGCACAATGGTGTTTATGTGAACATAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * ** * * *
5753351 ACCAAAGGTGAGAACTACTTTACGATGCTTAGAGAAATAAACAAACTTTGAGGTGAGAGCATCTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTG-GCATGTA
* *
5753416 CATTAACGTATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAT
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCC-----TAT
*
5753481 TATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAAACAAGGCATTCCTATTG
125 TATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTG
*
5753546 TGTAATAAAGGCACAATGGTGCTTATGTGAATATAT
190 TGTAATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * * * * ** *
5753582 A-CTTA-GTGAAAACCAATTTGTGGTGTTTAGAGAAATAAACCAACTTTGAGATGCAAGAATGTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTG-TGGCATGTA
* ** * *
5753645 TATTAAGGAATAATGTTGTGAATATGTGCATCT---ATTGGGTATTTGGTGCATTCCTATTATAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
* * *
5753707 AATTAAAGGTATAATGGTGCAAAACTAATATTTCATATATTAG-GAAGGCATTCCTATTATGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
* * *
5753771 TAAAGGCATAATAGTGCTTATGTGAATATAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * *
5753802 ACTTAAGGTGA-AA--ACTTTGTTGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGGGAATGTA
1 ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGT-GGCATGTA
* ** * * * *
5753864 CATTAAGGTATAACATTGCTAATATGTGAATCTAACATCGGGAATTTGGTACATTCCTATTACAC
65 CATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATAC
* *
5753929 AATTAAAGGTATAATGGTGC---A-T--T-TTT-AT-TA-T--ACAAGGCATTGCTATTGTGTAA
130 AATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAA
5753982 T-AAGGCACAATGGTGCTTATGTGAACATAT
195 TAAAGGCACAATGGTGCTTATGTGAACATAT
* * ** * *
5754012 TCATAAGGTGAGAATTACTTTGTGGTGCATT-GAGAAATAAACAAACTTTGAGGTGAGGGCATCT
1 ACCTAAGGTGAGAACCACTTTGTGGTGC-TTAGAGAAATAAACAAACTTTGAGGTG-TGGCATGT
* * * *
5754076 ACATTGAGGTATAATGTTGGCAATATGTGAATCTAACATCGGGTATTCGGTGCATTCCTATTATA
64 ACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATA
* * * **
5754141 CAATTGAAGGTATAATGGTGTTAAAA-TAATATTTCATATATTAAACTAGGC-CGCCTTATTGTG
129 CAATTGAAGGTATAATGGTG-CAAAACTAATATTTCATATATTAGACAAGGCATTCC-TATTGTG
* * *
5754204 TACTAAAAGAACAATGGTGCTTATGTGAACATAT
192 TAATAAAGGCACAATGGTGCTTATGTGAACATAT
* * ** *
5754238 ACAT-AGGTTGAGAACCACTTAGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGCAAGCATGA
1 ACCTAAGG-TGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTG-TGGCATGT
* * * *
5754302 ATATTAAGGAAAAATGTTGCCAATATGTGAATTTAACGTCGGGTATTTGGTGTGC-TT-CTATTA
64 ACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTT-G-GTGCATTCCTATTA
* * * * * *
5754365 TACAATAGAAGGTATAATGGTGCAAAACTAATATTTCATTTAATAGACAAGGAATTCTTATTGTC
127 TACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTG
* * *
5754430 TACTAAAGGAACAATGGTGCTTTTGTGAACATAT
192 TAATAAAGGCACAATGGTGCTTATGTGAACATAT
* * * *
5754464 ACAT-AGGATGAGAACCACTTTGTGGTGCTCAGAGAAATAAACAAACTTTGAGGTGTTGACGTGT
1 ACCTAAGG-TGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTG-TGGCATGT
* * *
5754528 ATATTAAGGAATAATGTTGCCAATATATGAATCTAACATCGGGTATTTGGTGCATTCCTATTACA
64 ACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATA
*
5754593 CAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTATACAAGGCATTCCTATTGTGTA
129 CAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTA
* *
5754658 ATAATGGCACAATGGTGCTTATGTGAGCATA
194 ATAAAGGCACAATGGTGCTTATGTGAACATA
5754689 CTTAAATGAA
Statistics
Matches: 3468, Mismatches: 414, Indels: 266
0.84 0.10 0.06
Matches are distributed among these distances:
202 41 0.01
204 35 0.01
205 3 0.00
206 3 0.00
207 1 0.00
209 3 0.00
210 38 0.01
211 27 0.01
212 4 0.00
213 123 0.04
214 249 0.07
215 12 0.00
216 3 0.00
217 10 0.00
218 130 0.04
219 149 0.04
220 197 0.06
221 59 0.02
222 55 0.02
223 5 0.00
224 27 0.01
225 36 0.01
226 1645 0.47
227 14 0.00
228 260 0.07
229 73 0.02
230 5 0.00
231 203 0.06
232 14 0.00
234 3 0.00
235 2 0.00
236 39 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (225 bp):
ACCTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGGCATGTAC
ATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTGCATTCCTATTATACA
ATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAAT
AAAGGCACAATGGTGCTTATGTGAACATAT
Found at i:5752818 original size:894 final size:883
Alignment explanation
Indices: 5750454--5755522 Score: 5066
Period size: 846 Copynumber: 5.7 Consensus size: 883
5750444 GTGGCTAACC
* * * * * * *
5750454 TAAGGTGAGAGCCACTTTGTGGTGCTTAGGGAAATAAACAAACTTTGAAGTGTGGCCATGTACAT
1 TAAGGTAAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGAGGGCATCTACAT
* * * * * *
5750519 TAAGGAATGATGTTGCCGATATGTGAATCTAACATCAGGAATTTGGTGCATTCTTATTGAACAAT
66 TAAGGTATAATGTTGCCGATATGTGAATCTAAC-TCGGGTATTTGGTGCATTCCTATT--ATAAT
* *
5750584 TGAAGGTATAATGGTGCAAAACTAATATTTC----A-TA-ACAAGGCATTCCTATTGTGTAATAA
128 TGAA-G-ATAATGGTGCAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTACTAA
* * * * * *
5750643 AGACACAATAGTGCTTATGTGAACATATTCCTAAGGTGAGAGCCACATTGTGGTGCTTAGAGAAA
191 AGGCACAATGGTGCTTATGTGAACATATACATAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAA
* * *
5750708 TAAACAAACTTTGAGATG-TGGCAATGTACATTAGGGAATAATGTTGCCAATATGTGAATCTAGC
256 TAAACAAACTTTGAGGTGCGGGC-ATG---A-T-----ATAATGTTGCCAATATGTGAATCTAAC
* * *
5750772 ATCGGGTACTTGATGCATTCC---TCTTATACAATTGAAGGTATAATGGTGCAAAACTAATATTT
311 ATCGGGTATTTGGTGCATTCCTTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTT
5750834 CATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATAC
376 CATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATAC
* * * *
5750899 CTAAGGTAAGAACCACTTTGT-CGTGC-TTAGAGAAATAAACAAACTTTGAGGTGCAGGCATATG
441 ATAA-GTGAGAACCACTTTGTGTGTGCTTTAGAGAAATAAACAAACTTTGAGGTGTAGGC--ATG
* *
5750962 TACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATCGGG-AGTTTGGTGCATTCCTATTA
503 TATATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTA-TTTGGTGCATTCCTATTA
* * * * *
5751026 CACAATTGAAGGTATAATGGTGCAAAACAAATATTTCATCTATTAGACAATGCATTTCTATTGTG
567 TACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTG
* * * * * * * *
5751091 TAATAAAGGCATAGTGGTGTTTAT-ACGAACATATACCTAAGGTGAGAGCCACTTTATGATGCTT
632 TAATAAAGGCACAATGGTGCTTATGTC-AACATATACTTAAGGTGAGAACCACTTTGTGGTGCTT
* * * *
5751155 AGAGAAATAAGCAAACTTTGAGGTGTGGGCATGTGCATTAAGGAATAATGTTGCCAATATGTGAA
696 AGAGAAATAAACAAACTTTGAGGTGAGGGCATGTACATTAAGGAATAATATTGCCAATATGTGAA
* * *
5751220 TCTAACGTTGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTACAATGGTACATTTCTATTA
761 TCTAACATTGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTATAATGGTACATTTTTATTA
*
5751285 TG-CAAGGCATTCCTATTGTGTAATAAA-GCAAAAATGGTG-TTAATGTGAACATATACT
826 TGACAAGGCATTCCTATTGTGTAATAAAGGC-ACAATGGTGCTT-ATGTGAACATATACT
* * *
5751342 TAAGGTCAA-AGCCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGTGGGCATGTACA
1 TAAGGT-AAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGAGGGCATCTACA
5751406 TTAAGGTATAATGTTGCCGATA--TG------A--C-GGTATTTGGTGCATTCCTATTATACAAT
65 TTAAGGTATAATGTTGCCGATATGTGAATCTAACTCGGGTATTTGGTGCATTCCTATTAT--AAT
* * ** * *
5751460 TTAAGGTATAATGGTGCAAAATTAATATTTCATCTATTAGATGAGGCATTCCTATTCTGTAATAA
128 TGAA-G-ATAATGGTGCAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTACTAA
* * * * * *
5751525 AGGCACAGTGGTGCTCATGTAAACATATACATAAGGTGAGAACCAGTTTGTGGTGTTTAGAAAAA
191 AGGCACAATGGTGCTTATGTGAACATATACATAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAA
* * *
5751590 TAAACAAACTTAGAGGTGTGGGCATGCATATTAAGGAATAATGTTGCCAATATGTGAATCTAAAA
256 TAAACAAACTTTGAGGTGCGGGCATG---A-T-----ATAATGTTGCCAATATGTGAATCTAACA
*
5751655 TCGGGTATTTGGTGCATTCC---TATTATACAATTGAAGGTATAATGGTGCCAAACTAATATTTC
312 TCGGGTATTTGGTGCATTCCTTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTC
* * *
5751717 ATATATTAGACAAGGCGTTCCTATTGTGTAATAAAGGCACAATGGTGCTCATGTAAACATATACA
377 ATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACA
* * * *
5751782 TAAGGTGAGAACCAGTTTGTG-GTG-TTTAGAAAAATAAACAAACTTAGAGGTGTGGGCATGTAT
442 TAA-GTGAGAACCACTTTGTGTGTGCTTTAGAGAAATAAACAAACTTTGAGGTGTAGGCATGTAT
5751845 ATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATACA
506 ATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATACA
* *
5751910 ATTGAAGGTATAATGGTGCCAAACTAATATTTCATATATTAGACAAGGCGTTCCTATTGTGTAAT
571 ATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAAT
* * * * * * *
5751975 AAAGGCACAATGGTGCTTATGTCAACATATGCATAAGGTGTGAACTACTTTGTGGTGCATATAAA
636 AAAGGCACAATGGTGCTTATGTCAACATATACTTAAGGTGAGAACCACTTTGTGGTGCTTAGAGA
* *
5752040 AATAAACAAACTTTGAGGTGAGGGCATCTACATTAAGGAATAATATTGGCAATATGTGAATCTAA
701 AATAAACAAACTTTGAGGTGAGGGCATGTACATTAAGGAATAATATTGCCAATATGTGAATCTAA
*** *
5752105 CATAACGTATTTGGTGCCTTCCTATTATACAATTGAAGGTATAATGGTACAAAACTAATATTTCA
766 CATTGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTATAATGGTAC---A-T--T-TTT-A
** * * *
5752170 TATATTAGACAAGGCATTTTTATTGTGTAATAAAGGTACAATGGTGCTTATATGAACAGATACT
823 T-TA-T-GACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACT
* * * *
5752234 TAAGGTAAGAACCACTTTGTGGTGTTTAGAGAAATAAACAAACTTTGAGGTGTGGGTATATGTAC
1 TAAGGTAAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGAGGG--CATCTAC
* * *
5752299 ATTAAGGAATAATGTTGCCGATATGTGAATCTAAACTCGAGTATTTGATGCATTCCTA-T-T-A-
64 ATTAAGGTATAATGTTGCCGATATGTGAATCT-AACTCGGGTATTTGGTGCATTCCTATTATAAT
* * * * * * *
5752360 TGCA-A-AATGGTGCAAAATTAATATTTAATGTATTAGAGAAGGCGTTCCTATTATATACTAAAG
128 TGAAGATAATGGTGCAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTACTAAAG
* * * * * * *
5752423 GGACAATGGTGCTAACT-TGAATATATACCTAAGAT-ATGAACCACTTTGTGGTGATTAGAGAAT
193 GCACAATGGTGCTTA-TGTGAACATATACATAAGGTGA-GAACCACTTTGTGGTGCTTAGAGAAA
* *
5752486 TAAACAAACTTTGAGGTGCGGGCATG-TAT-AT-TTGCCAATGTGTGAATCTAACATTGGGTATT
256 TAAACAAACTTTGAGGTGCGGGCATGATATAATGTTGCCAATATGTGAATCTAACATCGGGTATT
*
5752548 TGGTGCATTCCTATTATATTATACAATTGAAGGTATAATGGTGTAAAACTAATATTTCATATATT
321 TGGTGCATTCC--TTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATT
* *
5752613 AGACAAGACATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACTTAAGTGA
384 AGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACATAAGTGA
* * * * * *
5752678 TAGCCACTTTGTGGTTGTGGTCTTTGGAGAAATAAAC-AACTTTTGCGGTGTGGGCATGTACATT
449 GAACCACTTTGT-G-TGT-G-CTTTAGAGAAATAAACAAAC-TTTGAGGTGTAGGCATGTATATT
5752742 AAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATACAATT
509 AAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATACAATT
*
5752807 GAAGGTATAATGGTGCAAAACTAGTATTTCATATATTAGACATA-GCATTCCTATTGTGTAATAA
574 GAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACA-AGGCATTCCTATTGTGTAATAA
* ** * * * * *
5752871 GGGTGCAATGGTGCTTATATGAACATATATTTAAGATGAGAACCACTTTGTGGTGTTTAGAGAAA
638 AGGCACAATGGTGCTTATGTCAACATATACTTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAA
* * * * * *
5752936 TAAACAAACTTTGAGGTGTA-GGCATGTATATTAA-AACATAATGTTTCCAACATGTGAATCAAA
703 TAAACAAACTTTGAGGTG-AGGGCATGTACATTAAGGA-ATAATATTGCCAATATGTGAATCTAA
* * * * *
5752999 CATTTGGTGTTTAGTGCATTCCTATTATACAATTGAAGGTGTAATGGTTTAAAATTAATATTTCA
766 CATTGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTATAATGG--T-ACA-T--T-TTT-A
* * * * *
5753064 TATATTAGACAAGGCATTCCTATTGTGTAACAAAGGCACAATGGCGTTTATGTGAGCATATACC
823 T-TA-T-GACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACT
* * * *
5753128 TAAGGTAAGAACTACTTTATGGTGCTTAGAGAAATAAACAAACATTGAGGTGAGAGCATCTACAT
1 TAAGGTAAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGAGGGCATCTACAT
* *
5753193 TAACGTATAATGTTGCCGATATGTGAATCTAATGTCGGGTATTTGGTGCATTCCTATTATACAAT
66 TAAGGTATAATGTTGCCGATATGTGAATCTAA-CTCGGGTATTTGGTGCATTCCTATTAT--AAT
*
5753258 TGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAAC-A
128 TGAA-G-ATAATGGTGCAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGT-ACTA
* * ** *
5753322 AAGGCACAATGGTGTTTATGTGAACATATACCA-AAGGTGAGAACTACTTTACGATGCTTAGAGA
190 AAGGCACAATGGTGCTTATGTGAACATATA-CATAAGGTGAGAACCACTTTGTGGTGCTTAGAGA
* * *
5753386 AATAAACAAACTTTGAGGTGAGAGCATCTACATTAACGTATAATGTTGCCAATATGTGAATCTAA
254 AATAAACAAACTTTGAGGTGCG-G-----GCA-TGA--TATAATGTTGCCAATATGTGAATCTAA
5753451 CATCGGGTATTTGGTGCATTCCTATTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATA
310 CATCGGGTATTTGGTGCATTCC--TTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATA
* *
5753516 TTTCATATATTAAACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAATATA
373 TTTCATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATA
* * * * * * * *
5753581 TAC-TTAGTGAAAACCAATTTGTG-GTG-TTTAGAGAAATAAACCAACTTTGAGATGCAAGAATG
438 TACATAAGTGAGAACCACTTTGTGTGTGCTTTAGAGAAATAAACAAACTTTGAGGTGTAGGCATG
** * *
5753643 TATATTAAGGAATAATGTTGTGAATATGTGCATCT---ATTGGGTATTTGGTGCATTCCTATTAT
503 TATATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTAT
* * *
5753705 ACAATTAAAGGTATAATGGTGCAAAACTAATATTTCATATATTAG-GAAGGCATTCCTATTATGT
568 ACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGT
* * * * *
5753769 AATAAAGGCATAATAGTGCTTATGTGAATATATACTTAAGGTGA-AA--ACTTTGTTGTGCTTAG
633 AATAAAGGCACAATGGTGCTTATGTCAACATATACTTAAGGTGAGAACCACTTTGTGGTGCTTAG
* * * * *
5753831 AGAAATAAACAAACTTTGAGGTGTGGGAATGTACATTAAGGTATAACATTGCTAATATGTGAATC
698 AGAAATAAACAAACTTTGAGGTGAGGGCATGTACATTAAGGAATAATATTGCCAATATGTGAATC
* * * * * *
5753896 TAACATCGGGAATTTGGTACATTCCTATTACACAATTAAAGGTATAATGGTGCATTTTTATTAT-
763 TAACATTGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTATAATGGTACATTTTTATTATG
* * *
5753960 ACAAGGCATTGCTATTGTGTAAT-AAGGCACAATGGTGCTTATGTGAACATATTCA
828 ACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACT
* **
5754015 TAAGGTGAGAATTACTTTGTGGTGCATT-GAGAAATAAACAAACTTTGAGGTGAGGGCATCTACA
1 TAAGGTAAGAACCACTTTGTGGTGC-TTAGAGAAATAAACAAACTTTGAGGTGAGGGCATCTACA
* * * *
5754079 TTGAGGTATAATGTTGGCAATATGTGAATCTAACATCGGGTATTCGGTGCATTCCTATTATACAA
65 TTAAGGTATAATGTTGCCGATATGTGAATCTAAC-TCGGGTATTTGGTGCATTCCTATTAT--AA
* * * **
5754144 TTGAAGGTATAATGGTGTTAAAA-TAATATTTCATATATTAAACTAGGC-CGCCTTATTGTGTAC
127 TTGAA-G-ATAATGGTG-CAAAATTAATATTTCATATATTAGACAAGGCATTCC-TATTGTGTAC
* * *
5754207 TAAAAGAACAATGGTGCTTATGTGAACATATACAT-AGGTTGAGAACCACTTAGTGGTGCTTAGA
188 TAAAGGCACAATGGTGCTTATGTGAACATATACATAAGG-TGAGAACCACTTTGTGGTGCTTAGA
** *
5754271 GAAATAAACAAACTTTGAGGTGCAAGCATGAATATTAAGGAAAAATGTTGCCAATATGTGAATTT
252 GAAATAAACAAACTTTGAGGTGCGGGCATG-ATA-T-------AATGTTGCCAATATGTGAATCT
* * * *
5754336 AACGTCGGGTATTTGGTG---TGCTTCTATTATACAATAGAAGGTATAATGGTGCAAAACTAATA
308 AACATCGGGTATTTGGTGCATTCCTTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATA
* * * * * * * *
5754398 TTTCATTTAATAGACAAGGAATTCTTATTGTCTACTAAAGGAACAATGGTGCTTTTGTGAACATA
373 TTTCATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATA
* * * * *
5754463 TACATAGGATGAGAACCACTTTGTG-GTGC-TCAGAGAAATAAACAAACTTTGAGGTGTTGACGT
438 TACATAAG-TGAGAACCACTTTGTGTGTGCTTTAGAGAAATAAACAAACTTTGAGGTGTAGGCAT
* *
5754526 GTATATTAAGGAATAATGTTGCCAATATATGAATCTAACATCGGGTATTTGGTGCATTCCTATTA
502 GTATATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTA
* *
5754591 CACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTATACAAGGCATTCCTATTGTG
567 TACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTG
* * * *
5754656 TAATAATGGCACAATGGTGCTTATGTGAGC--ATACTTAA-AT--G-A--AC-TT-T-GTG-TT-
632 TAATAAAGGCACAATGGTGCTTATGTCAACATATACTTAAGGTGAGAACCACTTTGTGGTGCTTA
* * *
5754708 --G-----------C------G-GA---CATGTACATTAAGGAATAATGTTGCTAATATGCGAAT
697 GAGAAATAAACAAACTTTGAGGTGAGGGCATGTACATTAAGGAATAATATTGCCAATATGTGAAT
* * * *
5754750 CTAACATTGAGTATTTGGTGCATTCCTATTATACATTTGAAGGTGTAATGGTGCAAAATTGATAT
762 CTAACATTGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTATAATGGT---ACA-T--T-T
* * * * * *
5754815 TTCTTATAATAGAGATGACATTCCTATTGTGTAATAAATGCACAATGGTGTTTATCTGAACATAT
820 TTATTATGACA-AG--G-CATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATAT
*
5754880 ACC
881 ACT
* ** ** *
5754883 TAAGGTGAGGGCCTTTTTGTGGTGTTTAGAGAAATAAA-AATACTTT-A-GT-A----A--TA-A
1 TAAGGTAAGAACCACTTTGTGGTGCTTAGAGAAATAAACAA-ACTTTGAGGTGAGGGCATCTACA
* * *
5754937 -T---G-----T-TT-CC-ATTATGTGAATCAAAATTGGGTATTTGGTGCATTCCTATTATACAA
65 TTAAGGTATAATGTTGCCGA-TATGTGAATCTAACTCGGGTATTTGGTGCATTCCTATTAT--AA
* * * *
5754990 TTGAAGGTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTATTGTGTAATA
127 TTGAA-G-ATAATGGTGCAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTACTA
* * * *
5755055 AATGG-ACAATGGTGCTTATGTGAACATATACCTAAGGTGAGAATCATTTTGTGGTGCTTAGTGA
190 AA-GGCACAATGGTGCTTATGTGAACATATACATAAGGTGAGAACCACTTTGTGGTGCTTAGAGA
* * * * *
5755119 AATAAACAAAGTTTGAGGTGTGGGCATTTACATTAAGGAATGATGTTGCCAATTTGTGAATCTAA
254 AATAAACAAACTTTGAGGTGCGGGCA--T-GA-T-----ATAATGTTGCCAATATGTGAATCTAA
** * * *
5755184 CATCAAGTATTTGGTGCATTCC---TGTTATACAACTGAAGGTATAATGGTGCAAAACTAGTATT
310 CATCGGGTATTTGGTGCATTCCTTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATATT
* * * * * *
5755246 TCTTATATTAGACAAGACATTCCTGTTGTGTAATAAAAGCACAATGATGCTTATATGAACATATA
375 TCATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATA
** * * * ** *
5755311 TTTAAGATGAGAACCACTTTGTG-GTGC-CTAGTGAAATAAATAAACTTTGAGGTACAGGCATTT
440 CATAAG-TGAGAACCACTTTGTGTGTGCTTTAGAGAAATAAACAAACTTTGAGGTGTAGGCATGT
* * * * * *
5755374 ACATTGAGGAATAATGTTGCCAATATGTGAATCTAACATCGGCTATTTAGTGTATTCCTATTATA
504 ATATTAAGGAATAATGTTGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATA
* * * * * *
5755439 CATTTAAAGGTATAATGGTGCAAAACTTATATTTTATATATTAAACAAGGCATTCCTATTGTGGA
569 CAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTA
5755504 ATAAAGGCACAATGGTGCT
634 ATAAAGGCACAATGGTGCT
5755523 AAACAAATTT
Statistics
Matches: 3567, Mismatches: 464, Indels: 342
0.82 0.11 0.08
Matches are distributed among these distances:
845 4 0.00
846 458 0.13
847 19 0.01
848 4 0.00
849 4 0.00
853 1 0.00
854 2 0.00
855 76 0.02
857 1 0.00
858 3 0.00
859 4 0.00
861 2 0.00
862 7 0.00
863 2 0.00
864 2 0.00
865 2 0.00
866 3 0.00
867 21 0.01
868 60 0.02
874 1 0.00
876 52 0.01
877 1 0.00
879 4 0.00
880 284 0.08
881 8 0.00
882 395 0.11
883 9 0.00
884 116 0.03
885 3 0.00
886 22 0.01
887 367 0.10
888 161 0.05
889 107 0.03
890 2 0.00
891 10 0.00
892 153 0.04
893 11 0.00
894 443 0.12
895 3 0.00
896 126 0.04
897 5 0.00
898 4 0.00
900 109 0.03
901 3 0.00
902 115 0.03
903 56 0.02
904 70 0.02
905 2 0.00
906 17 0.00
907 56 0.02
908 5 0.00
909 2 0.00
910 2 0.00
912 4 0.00
913 17 0.00
914 147 0.04
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (883 bp):
TAAGGTAAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTGAGGTGAGGGCATCTACAT
TAAGGTATAATGTTGCCGATATGTGAATCTAACTCGGGTATTTGGTGCATTCCTATTATAATTGA
AGATAATGGTGCAAAATTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTACTAAAGGCA
CAATGGTGCTTATGTGAACATATACATAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAAC
AAACTTTGAGGTGCGGGCATGATATAATGTTGCCAATATGTGAATCTAACATCGGGTATTTGGTG
CATTCCTTATATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTAGACAAG
GCATTCCTATTGTGTAATAAAGGCACAATGGTGCTTATGTGAACATATACATAAGTGAGAACCAC
TTTGTGTGTGCTTTAGAGAAATAAACAAACTTTGAGGTGTAGGCATGTATATTAAGGAATAATGT
TGCCAATATGTGAATCTAAAATCGGGTATTTGGTGCATTCCTATTATACAATTGAAGGTATAATG
GTGCAAAACTAATATTTCATATATTAGACAAGGCATTCCTATTGTGTAATAAAGGCACAATGGTG
CTTATGTCAACATATACTTAAGGTGAGAACCACTTTGTGGTGCTTAGAGAAATAAACAAACTTTG
AGGTGAGGGCATGTACATTAAGGAATAATATTGCCAATATGTGAATCTAACATTGGGTATTTGGT
GCATTCCTATTATACAATTGAAGGTATAATGGTACATTTTTATTATGACAAGGCATTCCTATTGT
GTAATAAAGGCACAATGGTGCTTATGTGAACATATACT
Found at i:5754839 original size:190 final size:197
Alignment explanation
Indices: 5754525--5755096 Score: 662
Period size: 190 Copynumber: 2.9 Consensus size: 197
5754515 GGTGTTGACG
* * *
5754525 TGTATATTAAGGAATAATGTTGCCAATATATGAATCTAACATCGGGTATTTGGTGCATTCCTATT
1 TGTACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATTGGGTATTTGGTGCATTCCTATT
* * * *
5754590 ACACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATATATTATACAAGGCATTCCTATTGT
66 ATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTATTGT
* * *
5754655 GTAAT-AATGGCACAATGGTGCTTATGTGAGCATACTTAA-ATGA-AC-TT-T-GTGTTGCG-GA
131 GTAATAAATGGCACAATGGTGCTTATGTGAACATACCTAAGATGAGACTTTGTGGTGTTGAGAGA
*
5754713 CA
196 AA
* * *
5754715 TGTACATTAAGGAATAATGTTGCTAATATGCGAATCTAACATTGAGTATTTGGTGCATTCCTATT
1 TGTACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATTGGGTATTTGGTGCATTCCTATT
* * * * * * *
5754780 ATACATTTGAAGGTGTAATGGTGCAAAATTGATATTTCTTATAATAGAGATGACATTCCTATTGT
66 ATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTATTGT
* * * *
5754845 GTAATAAAT-GCACAATGGTGTTTATCTGAACATATACCTAAGGTGAGGGCCTTTTTGTGGTGTT
131 GTAATAAATGGCACAATGGTGCTTATGTGAAC--ATACCTAAGATGA--GAC--TTTGTGGTGTT
*
5754909 TAGAGAAA
190 GAGAGAAA
* * * * * *
5754917 TAAAAATAC-TTTAGTAATAATGTTTCCATTATGTGAATC-AAAATTGGGTATTTGGTGCATTCC
1 T----GTACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATTGGGTATTTGGTGCATTCC
5754980 TATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTA
62 TATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTA
*
5755045 TTGTGTAATAAATGG-ACAATGGTGCTTATGTGAACATATACCTAAGGTGAGA
127 TTGTGTAATAAATGGCACAATGGTGCTTATGTGAAC--ATACCTAAGATGAGA
5755097 ATCATTTTGT
Statistics
Matches: 319, Mismatches: 45, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
190 137 0.43
191 3 0.01
192 7 0.02
193 3 0.01
196 1 0.00
199 2 0.01
200 1 0.00
201 6 0.02
202 5 0.02
204 126 0.39
205 25 0.08
206 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (197 bp):
TGTACATTAAGGAATAATGTTGCCAATATGTGAATCTAACATTGGGTATTTGGTGCATTCCTATT
ATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTATTGT
GTAATAAATGGCACAATGGTGCTTATGTGAACATACCTAAGATGAGACTTTGTGGTGTTGAGAGA
AA
Found at i:5755110 original size:204 final size:205
Alignment explanation
Indices: 5754727--5755358 Score: 665
Period size: 204 Copynumber: 3.0 Consensus size: 205
5754717 TACATTAAGG
* * *
5754727 AATAATGTTGCTAATATGCGAATCTAACATTGAGTATTTGGTGCATTCCTATTATACATTTGAAG
1 AATAATGTTGCCAATATGCGAATCTAAAATTGAGTATTTGGTGCATTCCTATTATACAATTGAAG
* * * * *
5754792 GTGTAATGGTGCAAAATTGATATTTCTTATAATAGAGATGACATTCCTATTGTGTAATAAATGCA
66 GTATAATGGTGCAAAACTAATATTTCTTATAATAGACAAGACATTCCTATTGTGTAATAAATGCA
* ** * *
5754857 CAATGGTGTTTATCTGAACATATACCTAAGGTGAGGGCCTTTTTGTGGTGTTTAGAGAAATAAAA
131 CAATGGTGCTTATCTGAACATATACCTAAGGTGAGAACCATTTTGTGGTGCTTAGAGAAATAAAA
5754922 ATACTTTAGT
196 ATACTTTAGT
* * * *
5754932 AATAATGTTTCCATTATGTGAATC-AAAATTGGGTATTTGGTGCATTCCTATTATACAATTGAAG
1 AATAATGTTGCCAATATGCGAATCTAAAATTGAGTATTTGGTGCATTCCTATTATACAATTGAAG
* *
5754996 GTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTATTGTGTAATAAATGGA
66 GTATAATGGTGCAAAACTAATATTTCTTATAATAGACAAGACATTCCTATTGTGTAATAAATGCA
* * *
5755061 CAATGGTGCTTATGTGAACATATACCTAAGGTGAGAATCATTTTGTGGTGCTTAGTGAAATAAAC
131 CAATGGTGCTTATCTGAACATATACCTAAGGTGAGAACCATTTTGTGGTGCTTAGAGAAAT-AA-
*
5755126 AAAGTTTGAGGTGTGGGCATTTACATT
194 AAA---T-A--------C-TTT--AGT
* * * * ** * *
5755153 AAGGAATGATGTTGCCAATTTGTGAATCTAACATCAAGTATTTGGTGCATTCCTGTTATACAACT
1 AA--TA--ATGTTGCCAATATGCGAATCTAAAATTGAGTATTTGGTGCATTCCTATTATACAATT
* * *
5755218 GAAGGTATAATGGTGCAAAACTAGTATTTCTTATATTAGACAAGACATTCCTGTTGTGTAATAAA
62 GAAGGTATAATGGTGCAAAACTAATATTTCTTATAATAGACAAGACATTCCTATTGTGTAATAAA
* * * ** * * * *
5755283 AGCACAATGATGCTTATATGAACATATATTTAAGATGAGAACCACTTTGTGGTGCCTAGTGAAAT
127 TGCACAATGGTGCTTATCTGAACATATACCTAAGGTGAGAACCATTTTGTGGTGCTTAGAGAAAT
5755348 AAATAA-ACTTT
192 AAA-AATACTTT
5755359 GAGGTACAGG
Statistics
Matches: 359, Mismatches: 45, Indels: 40
0.81 0.10 0.09
Matches are distributed among these distances:
204 148 0.41
205 22 0.06
206 3 0.01
209 1 0.00
210 1 0.00
211 3 0.01
212 1 0.00
218 1 0.00
219 3 0.01
220 1 0.00
221 4 0.01
223 1 0.00
224 1 0.00
225 21 0.06
226 148 0.41
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (205 bp):
AATAATGTTGCCAATATGCGAATCTAAAATTGAGTATTTGGTGCATTCCTATTATACAATTGAAG
GTATAATGGTGCAAAACTAATATTTCTTATAATAGACAAGACATTCCTATTGTGTAATAAATGCA
CAATGGTGCTTATCTGAACATATACCTAAGGTGAGAACCATTTTGTGGTGCTTAGAGAAATAAAA
ATACTTTAGT
Found at i:5755362 original size:226 final size:224
Alignment explanation
Indices: 5754932--5755522 Score: 790
Period size: 226 Copynumber: 2.6 Consensus size: 224
5754922 ATACTTTAGT
* * * **
5754932 AATAATGTTTCCATTATGTGAATC-AAAATTGGGTATTTGGTGCATTCCTATTATACAATTGAAG
1 AATAATGTTGCCAATATGTGAATCTAACA-TCAGTATTTGGTGCATTCCTATTATACAATTGAAG
* *
5754996 GTATAATGGTGCAAAACTAATATTTCTTATATTAGACAAGACATTCCTATTGTGTAATAAATGGA
65 GTATAATGGTGCAAAACT-ATATTTCTTATATTAGACAAGACATTCCTATTGTGTAATAAAAGCA
* * * * *
5755061 CAATGGTGCTTATGTGAACATATACCTAAGGTGAGAATCATTTTGTGGTGCTTAGTGAAATAAAC
129 CAATGGTGCTTATATGAACATATACCTAAGATGAGAACCACTTTGTGGTGCCTAGTGAAATAAAC
* ***
5755126 AAAGTTTGAGGTGTGGGCATTTACATTAAGG
194 AAACTTTGAGGTACAGGCATTTACATTAAGG
* * * *
5755157 AATGATGTTGCCAATTTGTGAATCTAACATCAAGTATTTGGTGCATTCCTGTTATACAACTGAAG
1 AATAATGTTGCCAATATGTGAATCTAACATC-AGTATTTGGTGCATTCCTATTATACAATTGAAG
*
5755222 GTATAATGGTGCAAAACTAGTATTTCTTATATTAGACAAGACATTCCTGTTGTGTAATAAAAGCA
65 GTATAATGGTGCAAAACTA-TATTTCTTATATTAGACAAGACATTCCTATTGTGTAATAAAAGCA
* ** *
5755287 CAATGATGCTTATATGAACATATATTTAAGATGAGAACCACTTTGTGGTGCCTAGTGAAATAAAT
129 CAATGGTGCTTATATGAACATATACCTAAGATGAGAACCACTTTGTGGTGCCTAGTGAAATAAAC
*
5755352 AAACTTTGAGGTACAGGCATTTACATTGAGG
194 AAACTTTGAGGTACAGGCATTTACATTAAGG
* * * * *
5755383 AATAATGTTGCCAATATGTGAATCTAACATCGGCTATTTAGTGTATTCCTATTATACATTTAAAG
1 AATAATGTTGCCAATATGTGAATCTAACATCAG-TATTTGGTGCATTCCTATTATACAATTGAAG
* * * *
5755448 GTATAATGGTGCAAAACTTATATTT-TATATATTAAACAAGGCATTCCTATTGTGGAATAAAGGC
65 GTATAATGGTGCAAAAC-TATATTTCT-TATATTAGACAAGACATTCCTATTGTGTAATAAAAGC
5755512 ACAATGGTGCT
128 ACAATGGTGCT
5755523 AAACAAATTT
Statistics
Matches: 319, Mismatches: 41, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
225 24 0.08
226 293 0.92
227 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (224 bp):
AATAATGTTGCCAATATGTGAATCTAACATCAGTATTTGGTGCATTCCTATTATACAATTGAAGG
TATAATGGTGCAAAACTATATTTCTTATATTAGACAAGACATTCCTATTGTGTAATAAAAGCACA
ATGGTGCTTATATGAACATATACCTAAGATGAGAACCACTTTGTGGTGCCTAGTGAAATAAACAA
ACTTTGAGGTACAGGCATTTACATTAAGG
Found at i:5755664 original size:175 final size:175
Alignment explanation
Indices: 5755373--5755694 Score: 464
Period size: 175 Copynumber: 1.8 Consensus size: 175
5755363 TACAGGCATT
* * * *
5755373 TACATTGAGGAATAATGTTGCCAATATGTGAATCTAACATCGGCTATTTAGTGTATTCCTATTAT
1 TACATTAAGGAATAAAGCTGCCAATATGTGAATCTAACATCGGCTATTTAGTGCATTCCTATTAT
* * * *
5755438 ACATTTAAAGGTATAATGGTGCAAAACTTATATTTTATATATTAAACAAGGCATTCCTATTGTGG
66 ACAATTAAAGGTATAATGGTGCAAAACTAATATTTCATATATTAAACAAGGCATTCCTATTGTAG
5755503 AATAAAGGCACAATGGTGCTAAACAAATTTTGAGGTGCAAACATG
131 AATAAAGGCACAATGGTGCTAAACAAATTTTGAGGTGCAAACATG
* * * * *
5755548 TACATTAAGGAATAAAGCTGGCAATATGTGAATCTAACATTGGGTATTTGGTGCATTTCTATTAT
1 TACATTAAGGAATAAAGCTGCCAATATGTGAATCTAACATCGGCTATTTAGTGCATTCCTATTAT
* * * ** *
5755613 ACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATTTATTAGACAAGGCATTTTTATTGTAT
66 ACAATTAAAGGTATAATGGTGCAAAACTAATATTTCATATATTAAACAAGGCATTCCTATTGTAG
*
5755678 AATAAAGGCACAGTGGT
131 AATAAAGGCACAATGGT
5755695 ACTTATGTGA
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
175 127 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (175 bp):
TACATTAAGGAATAAAGCTGCCAATATGTGAATCTAACATCGGCTATTTAGTGCATTCCTATTAT
ACAATTAAAGGTATAATGGTGCAAAACTAATATTTCATATATTAAACAAGGCATTCCTATTGTAG
AATAAAGGCACAATGGTGCTAAACAAATTTTGAGGTGCAAACATG
Found at i:5756297 original size:230 final size:227
Alignment explanation
Indices: 5755544--5756366 Score: 879
Period size: 226 Copynumber: 3.6 Consensus size: 227
5755534 GAGGTGCAAA
* * * * * *
5755544 CATGTACATTAAGGAATAAAGCTGGCAATATGTGAATCTAACAT-TGGGTATTTGGTGCATTTCT
1 CATGTACATTAAGGTATAATGTTGCCAATATGTGAATCTAACATAT-CGTATTTGGTGCATTCCT
* * * **
5755608 ATTATACAATTGAAGGTATAATGGTGCAAAACTAATATTTCATTTATTAGACAAGGCATTTTTAT
65 ATTATACAATTGAAGGTATAATGGTGCAAAATTAATATTTCATATATTAGATAAGGCATTCCTAT
* * * * * * *
5755673 TGTATAAT-AAAGGCACAGTGGTACTTATGTGAACATATACTTAAGCTGAGAATTACTTTATGGT
130 TGTGTAATAAAAGGCACAATGGTGCTTATGTGAACATATACCTAAGATAAG-AGTACTTTATGGT
* * **
5755737 GCTTAGAGAAATAAACAAAG-TTTGAGATGT-GCA
194 GCTTAAAGAAATAAAC-AAGCTTTGAGGTGTGGGG
* * * * *
5755770 CTTGTATAGTAAGGTATAATGTTGCCAATATGTGAATCTAACATCA-GGTATTTGGTGTATTCCT
1 CATGTACATTAAGGTATAATGTTGCCAATATGTGAATCTAACAT-ATCGTATTTGGTGCATTCCT
* * * *
5755834 TTTATACAATTGAATGTATAATGGTGCAAAATTAATATTCCATATATTAGATAAGGCATACCTAT
65 ATTATACAATTGAAGGTATAATGGTGCAAAATTAATATTTCATATATTAGATAAGGCATTCCTAT
* * *
5755899 TGTGTAATAAAA-GCACAATGGTGCTTATGTAAACATATACCTAAGATGATA-AGTAGTTTATGA
130 TGTGTAATAAAAGGCACAATGGTGCTTATGTGAACATATACCTAAGAT-A-AGAGTACTTTATGG
* * *
5755962 TGCTTAAGGAAATAAACAAACTTTGAGTTGT-GGG
193 TGCTTAAAGAAATAAACAAGCTTTGAGGTGTGGGG
* * * ** * * *
5755996 CATGTAAATTAAGGTATAATGTTGCCAGTATGTGAATTTGTCATCTCGTATTTGGTGCATTCATG
1 CATGTACATTAAGGTATAATGTTGCCAATATGTGAATCTAACATATCGTATTTGGTGCATTCCTA
* * * * * *
5756061 TTATACAATTGAAGGCATAATGGCGCAAAATTGATATTTCATATGTTTGATAGGGCATTCCTATT
66 TTATACAATTGAAGGTATAATGGTGCAAAATTAATATTTCATATATTAGATAAGGCATTCCTATT
* ** * * *
5756126 CTGTTGTAAAAGGCACAATAGTGCTTATGTGAACATATACCTAAGGTAAGAGTCACTTTTTGGTG
131 GTGTAATAAAAGGCACAATGGTGCTTATGTGAACATATACCTAAGATAAGAGT-ACTTTATGGTG
*
5756191 CTTAAAGAAATAAACAAGCTTTAAGGTGTGGGTGG
195 CTTAAAGAAATAAACAAGCTTTGAGGTGT-GG-GG
* *
5756226 CATGTACATTAAGGTATAATGTTACCAATATGTGAATCTAACATATCGTATTTGGCGCATTCCTA
1 CATGTACATTAAGGTATAATGTTGCCAATATGTGAATCTAACATATCGTATTTGGTGCATTCCTA
* * * * * * * * *
5756291 TTATACAATTGAAGGTATAATTGTGCAAGATTAATATTTTATATGTTTGACATGACATTCTTATT
66 TTATACAATTGAAGGTATAATGGTGCAAAATTAATATTTCATATATTAGATAAGGCATTCCTATT
*
5756356 GTGTAAGAAAA
131 GTGTAATAAAA
5756367 CATATATTAG
Statistics
Matches: 492, Mismatches: 92, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
225 3 0.01
226 300 0.61
227 68 0.14
228 1 0.00
229 1 0.00
230 119 0.24
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (227 bp):
CATGTACATTAAGGTATAATGTTGCCAATATGTGAATCTAACATATCGTATTTGGTGCATTCCTA
TTATACAATTGAAGGTATAATGGTGCAAAATTAATATTTCATATATTAGATAAGGCATTCCTATT
GTGTAATAAAAGGCACAATGGTGCTTATGTGAACATATACCTAAGATAAGAGTACTTTATGGTGC
TTAAAGAAATAAACAAGCTTTGAGGTGTGGGG
Found at i:5756792 original size:227 final size:226
Alignment explanation
Indices: 5756367--5756863 Score: 624
Period size: 227 Copynumber: 2.2 Consensus size: 226
5756357 TGTAAGAAAA
* * * * * * *
5756367 CATATATTAGACAAGGCATTCTTATTGTGTAATAAAGGCACAATAATGCTTATGTGAACATATAT
1 CATATATTATACAAGGCATTTTTATTGTGTAATAAAGACACAATAATGATAATGTGAACATACAC
* * * * *
5756432 CTAAGTTGAAAACTACTTTGTTGTGTTTAAAACAATATACAAATTTTGATGTATGGGCATGTACA
66 CTAAGGTGAAAACTACTTTGTGGTGCTTAAAACAATAAACAAATTTTGAGGTATGGGCATGTACA
* * * *
5756497 TTAAGCTATAATGTTGTTAATATGTGAATCTAAGATTAGGTATTTAGTGCATTCCTATTATACAA
131 TTAAGCTATAATGTTGTCAATATATGAATCTAACATTAGGTATTTAGTGCAATCCTATTATACAA
*
5756562 TTGAAGGCATAATGTTGCAAAACTAATATTC
196 TTGAAGGCATAATGGTGCAAAACTAATATTC
* *
5756593 CATATATTATACAAGACATTTTTATTGTGTAATAAAGACACAATAGTGATAATGTGAACATACAC
1 CATATATTATACAAGGCATTTTTATTGTGTAATAAAGACACAATAATGATAATGTGAACATACAC
* * *
5756658 CTAAGGTGAGAACTACTTTGTGGTGCTTAGAGA-AATAAACAAACTTTTGAGGTGTGGGCATGTA
66 CTAAGGTGAAAACTACTTTGTGGTGCTTA-AAACAATAAACAAA-TTTTGAGGTATGGGCATGTA
* *
5756722 TATTAAGGTATAATGTTGTCAATATATGAATCTAACATCT-GGTATTTGACG-G-AATCCTATTA
129 CATTAAGCTATAATGTTGTCAATATATGAATCTAACAT-TAGGTATTT-A-GTGCAATCCTATTA
* ** * *
5756784 TACAATTGAAGGTATAATGGTGCAAAGTTGATATTT
191 TACAATTGAAGGCATAATGGTGCAAAACTAATATTC
* * * *
5756820 CATATATTTTATAAGGCATTTCTATTGTGTAATAATGACACAAT
1 CATATATTATACAAGGCATTTTTATTGTGTAATAAAGACACAAT
5756864 GGTTTTTATG
Statistics
Matches: 232, Mismatches: 34, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
226 90 0.39
227 138 0.59
228 3 0.01
229 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (226 bp):
CATATATTATACAAGGCATTTTTATTGTGTAATAAAGACACAATAATGATAATGTGAACATACAC
CTAAGGTGAAAACTACTTTGTGGTGCTTAAAACAATAAACAAATTTTGAGGTATGGGCATGTACA
TTAAGCTATAATGTTGTCAATATATGAATCTAACATTAGGTATTTAGTGCAATCCTATTATACAA
TTGAAGGCATAATGGTGCAAAACTAATATTC
Found at i:5774276 original size:24 final size:23
Alignment explanation
Indices: 5774239--5774292 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
5774229 CTTTTTTTTT
* *
5774239 TTCTTGTATTGTAAAGTTTCATCC
1 TTCTTGTATAGTAAAATTTCAT-C
*
5774263 TTCTTTTATAGTAAAATTTCATC
1 TTCTTGTATAGTAAAATTTCATC
5774286 TTCTTGT
1 TTCTTGT
5774293 CATTTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (23 bp):
TTCTTGTATAGTAAAATTTCATC
Found at i:5778233 original size:76 final size:76
Alignment explanation
Indices: 5778107--5778257 Score: 248
Period size: 76 Copynumber: 2.0 Consensus size: 76
5778097 ATTCAGATGT
*
5778107 CATCTTATAATAAACAAACCTCAAAGTATCAGTTAATATATGAAGAGCTGCTTTAGATGCAGTGT
1 CATCTTATAATAAACAAACCTCAAAGTATCAGTTAATACATGAAGAGCTGCTTTAGATGCAGTGT
*
5778172 AGGCACCAGAA
66 AGACACCAGAA
* * * *
5778183 CATCTTCTAATAAACTAACCTCAGAGTATCAGTTAATGCATGAAGAGCTGCTTTAGATGCAGTGT
1 CATCTTATAATAAACAAACCTCAAAGTATCAGTTAATACATGAAGAGCTGCTTTAGATGCAGTGT
5778248 AGACACCAGA
66 AGACACCAGA
5778258 CCATGGCCCA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (76 bp):
CATCTTATAATAAACAAACCTCAAAGTATCAGTTAATACATGAAGAGCTGCTTTAGATGCAGTGT
AGACACCAGAA
Found at i:5783722 original size:15 final size:16
Alignment explanation
Indices: 5783702--5783743 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
5783692 ATATTTTCAC
*
5783702 TTAATAATTTAAA-AA
1 TTAATATTTTAAAGAA
*
5783717 TTAATATTTTAAAGTA
1 TTAATATTTTAAAGAA
5783733 TTAATATTTTA
1 TTAATATTTTA
5783744 TTTATAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAATATTTTAAAGAA
Found at i:5783790 original size:30 final size:27
Alignment explanation
Indices: 5783724--5783793 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 27
5783714 AAATTAATAT
* *
5783724 TTTAAAGTATTAATATTTTATTTATAG
1 TTTAAAATATTAATATTTTATTTATAA
*
5783751 TTT-AAATATTAATATTTTTTAATTTTTAA
1 TTTAAAATATTAATA--TTTT-ATTTATAA
5783780 TTTAAAATATTAAT
1 TTTAAAATATTAAT
5783794 TTTATAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.28
27 3 0.08
28 4 0.11
29 9 0.25
30 10 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTAAAATATTAATATTTTATTTATAA
Found at i:5786104 original size:22 final size:18
Alignment explanation
Indices: 5786075--5786120 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 18
5786065 TTCCCTTTTT
5786075 ATAAAATTTTTTAAAAATATA
1 ATAAAA-TTTTT-AAAAT-TA
5786096 ATAATAATTTTTAAAATTA
1 ATAA-AATTTTTAAAATTA
5786115 ATAAAA
1 ATAAAA
5786121 AATAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 5 0.21
21 9 0.38
22 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAATTTTTAAAATTA
Found at i:5796496 original size:29 final size:27
Alignment explanation
Indices: 5796482--5796573 Score: 82
Period size: 30 Copynumber: 3.3 Consensus size: 27
5796472 AAAGAAATAG
* * *
5796482 TTGTTACACGTCAT-GTATAAAAA-CA
1 TTGTTACACGTCATATTAAAAAAATTA
*
5796507 -TGTTACACGTCATATTAAAAAAAATGTTG
1 TTGTTACACGTCATATT-AAAAAAA--TTA
5796536 TTGTTACACGTCATATTGAAAAAATATTA
1 TTGTTACACGTCATATT-AAAAAA-ATTA
5796565 TTGTTACAC
1 TTGTTACAC
5796574 ACTATGTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
24 13 0.24
25 1 0.02
26 6 0.11
29 11 0.20
30 22 0.41
31 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (27 bp):
TTGTTACACGTCATATTAAAAAAATTA
Found at i:5796511 original size:24 final size:23
Alignment explanation
Indices: 5796483--5796527 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
5796473 AAGAAATAGT
*
5796483 TGTTACACGTCATGTATAAAAACA
1 TGTTACACGTCATAT-TAAAAACA
5796507 TGTTACACGTCATATTAAAAA
1 TGTTACACGTCATATTAAAAA
5796528 AAATGTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (23 bp):
TGTTACACGTCATATTAAAAACA
Found at i:5796513 original size:83 final size:81
Alignment explanation
Indices: 5796296--5796534 Score: 231
Period size: 80 Copynumber: 2.9 Consensus size: 81
5796286 ATGATGTTAC
* * * *
5796296 ACACTATGTT-AAAAAAAATATTATTGTTACACTCTATATACAAAAACATGTTATACGTTATAGT
1 ACACCATGTTCAAAAAACATA-TGTTGTTACACTC-ATATACAAAAACATGTTACACGTTATAGT
* ***
5796360 T--AAAAAAGGTTTGTAT
64 TAAAAAAAATGTTCACAT
* *
5796376 ACACTATGTTCAAAAAACATATGTTGTTTTACA-TCATATACAAAAACATATTACACGTTATAGT
1 ACACCATGTTCAAAAAACATATGTTG--TTACACTCATATACAAAAACATGTTACACGTTATAGT
5796440 TAAAAAATAATGTTACACAT
64 TAAAAAA-AATGTT-CACAT
* * * *
5796460 ACACCATGTTGAAAAGAA-ATA-GTTGTTACACGTCATGTATAAAAACATGTTACACGTCATA-T
1 ACACCATGTTCAAAA-AACATATGTTGTTACAC-TCATATACAAAAACATGTTACACGTTATAGT
5796522 TAAAAAAAATGTT
64 TAAAAAAAATGTT
5796535 GTTGTTACAC
Statistics
Matches: 135, Mismatches: 14, Indels: 19
0.80 0.08 0.11
Matches are distributed among these distances:
80 42 0.31
81 22 0.16
82 17 0.13
83 34 0.25
84 18 0.13
85 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (81 bp):
ACACCATGTTCAAAAAACATATGTTGTTACACTCATATACAAAAACATGTTACACGTTATAGTTA
AAAAAAATGTTCACAT
Found at i:5796528 original size:24 final size:24
Alignment explanation
Indices: 5796483--5796534 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5796473 AAGAAATAGT
*
5796483 TGTTACACGTCATGTATAAAAACA
1 TGTTACACGTCATGTATAAAAAAA
*
5796507 TGTTACACGTCATAT-TAAAAAAAA
1 TGTTACACGTCATGTAT-AAAAAAA
5796531 TGTT
1 TGTT
5796535 GTTGTTACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (24 bp):
TGTTACACGTCATGTATAAAAAAA
Found at i:5796543 original size:30 final size:30
Alignment explanation
Indices: 5796507--5796590 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
5796497 TATAAAAACA
* *
5796507 TGTTACACGTCATATTAAAAAAAATGTTGT
1 TGTTACACGTCATATTAAAAAAAATATTAT
*
5796537 TGTTACACGTCATATT-GAAAAAATATTAT
1 TGTTACACGTCATATTAAAAAAAATATTAT
* *
5796566 TGTTACAC-ACTATGTTAAAAAAAAT
1 TGTTACACGTC-ATATTAAAAAAAAT
5796591 TTTTTTACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 22 0.48
30 23 0.50
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (30 bp):
TGTTACACGTCATATTAAAAAAAATATTAT
Found at i:5803297 original size:2 final size:2
Alignment explanation
Indices: 5803286--5803314 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5803276 GCACTCGACT
5803286 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5803315 AGGAAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5803401 original size:120 final size:120
Alignment explanation
Indices: 5803185--5803411 Score: 436
Period size: 120 Copynumber: 1.9 Consensus size: 120
5803175 TTTTATCATC
5803185 TATATATATAAGGAAATGTAAATGCTATATTCCAATGTTAACCTCTTTTGCCTTATTAGAGCTAA
1 TATATATATAAGGAAATGTAAATGCTATATTCCAATGTTAACCTCTTTTGCCTTATTAGAGCTAA
*
5803250 AAGAATGTGAAAAATCAAATTATATTGCACTCGACTTATATAATATATATATATA
66 AAGAATGTGAAAAATCAAATTATATTACACTCGACTTATATAATATATATATATA
*
5803305 TATATATATAAGGAAATGTAAATGTTATATTCCAATGTTAACCTCTTTTGCCTTATTAGAGCTAA
1 TATATATATAAGGAAATGTAAATGCTATATTCCAATGTTAACCTCTTTTGCCTTATTAGAGCTAA
5803370 AAGAATGTGAAAAATCAAATTATATTACACTCGACTTATATA
66 AAGAATGTGAAAAATCAAATTATATTACACTCGACTTATATA
5803412 TAATAATCAA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 105 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (120 bp):
TATATATATAAGGAAATGTAAATGCTATATTCCAATGTTAACCTCTTTTGCCTTATTAGAGCTAA
AAGAATGTGAAAAATCAAATTATATTACACTCGACTTATATAATATATATATATA
Found at i:5805796 original size:20 final size:20
Alignment explanation
Indices: 5805757--5805796 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5805747 AATAATTCTG
* * *
5805757 TTTCCTCTCGTCAAATTCAT
1 TTTCCTCTCATAAAAGTCAT
5805777 TTTCCTCTCATAAAAGTCAT
1 TTTCCTCTCATAAAAGTCAT
5805797 CCTCCATTAA
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:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTCCTCTCATAAAAGTCAT
Found at i:5811927 original size:214 final size:217
Alignment explanation
Indices: 5811572--5812027 Score: 559
Period size: 214 Copynumber: 2.1 Consensus size: 217
5811562 CAAATTATGC
*
5811572 ATAAATTAAATATATGTATATATAATAAATTACTTTATTATATATATGACATTAACGACACAACT
1 ATAAATTAAATATATGTATATATAATAAATTACTTTATTATATATATGAAATTAACGACACAACT
* * *
5811637 TATATGTTATAATATTTTAATTTTTATATCATAGTTTGTAGAAATAATAATTAATTATAAATAAT
66 TATATGTTATAATATTTTAA---TTATATCAAAGTTTGTAGAAATAATAACTAATTATAAACAAT
* *
5811702 CTGTTATAAAAACTAAGACAATAACTAAAAAAATTATTAAGTGTAATCATAT-AAATAAAGTCTA
128 ATATTATAAAAACTAAGACAATAACTAAAAAAATTATTAAGTGTAATCATATAAAATAAAGTCTA
*
5811766 TTATAACTTACAGTAATATTTATAT
193 TTATAACTTACAGTAATACTTATAT
* * ** *
5811791 ATAAATTAAATATATGTATATTTATTTTA-TATCTTTATTATGTATATATGAAATTAATGACACA
1 ATAAATTAAATATATGTATATATAATAAATTA-CTTTATTA--TATATATGAAATTAACGACACA
* * *
5811855 ACTTATATTTTATAATGTTTT-A-TAT-T-AAAGTTTGTATAAATAATAACTAATTATAAACAAT
63 ACTTATATGTTATAATATTTTAATTATATCAAAGTTTGTAGAAATAATAACTAATTATAAACAAT
*** * * ** *
5811916 ATATTATAAAAACTAAGGTGATAATTAATAAGGTTATTAAGTGTAATCATATAAAATAAAGTTTA
128 ATATTATAAAAACTAAGACAATAACTAAAAAAATTATTAAGTGTAATCATATAAAATAAAGTCTA
* * * *
5811981 TTATAAGTTATAGTACTACTTATGT
193 TTATAACTTACAGTAATACTTATAT
5812006 ATAAATTAAA-ATAT-TATATATA
1 ATAAATTAAATATATGTATATATA
5812028 TATATATGTT
Statistics
Matches: 205, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
213 7 0.03
214 78 0.38
215 42 0.20
216 3 0.01
218 2 0.01
219 33 0.16
220 1 0.00
221 39 0.19
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (217 bp):
ATAAATTAAATATATGTATATATAATAAATTACTTTATTATATATATGAAATTAACGACACAACT
TATATGTTATAATATTTTAATTATATCAAAGTTTGTAGAAATAATAACTAATTATAAACAATATA
TTATAAAAACTAAGACAATAACTAAAAAAATTATTAAGTGTAATCATATAAAATAAAGTCTATTA
TAACTTACAGTAATACTTATAT
Found at i:5812390 original size:12 final size:12
Alignment explanation
Indices: 5812373--5812416 Score: 70
Period size: 12 Copynumber: 3.5 Consensus size: 12
5812363 TGGCCAATTT
5812373 TTATATTATATA
1 TTATATTATATA
5812385 TTATATTATATA
1 TTATATTATATA
5812397 TTATATATATATA
1 TTATAT-TATATA
5812410 TATATAT
1 T-TATAT
5812417 AATTAGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 7 0.23
14 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATATTATATA
Found at i:5812396 original size:2 final size:2
Alignment explanation
Indices: 5812374--5812417 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
5812364 GGCCAATTTT
5812374 TA TA T- TA TA TA T- TA TA T- TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5812412 TA TA TA
1 TA TA TA
5812418 ATTAGTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5812398 original size:19 final size:19
Alignment explanation
Indices: 5812374--5812416 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5812364 GGCCAATTTT
5812374 TATATTATATAT-TATATTA
1 TATATTATATATATATA-TA
5812393 TATATTATATATATATATA
1 TATATTATATATATATATA
5812412 TATAT
1 TATAT
5812417 AATTAGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATATATATATA
Found at i:5822068 original size:26 final size:26
Alignment explanation
Indices: 5822007--5822072 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 26
5821997 ATTAAAAAAA
5822007 TTTAAAT-AAATTTTTATTCTTTTAT
1 TTTAAATCAAATTTTTATTCTTTTAT
* *
5822032 TACGTTCAATCAAATTTTTATTTTTTTAT
1 T---TTAAATCAAATTTTTATTCTTTTAT
5822061 TTTAAATCAAAT
1 TTTAAATCAAAT
5822073 AAATTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 1 0.03
26 10 0.29
28 5 0.15
29 18 0.53
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTAAATCAAATTTTTATTCTTTTAT
Found at i:5822079 original size:30 final size:29
Alignment explanation
Indices: 5822010--5822082 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
5822000 AAAAAAATTT
**
5822010 AAATAAATTTTTATTCTTTTATTACGTTC
1 AAATAAATTTTTATTCTTTTATTACAATC
*
5822039 -AATCAAATTTTTATTTTTTTATTTTA-AATC
1 AAAT-AAATTTTTATTCTTTTA--TTACAATC
5822069 AAATAAATTTTTAT
1 AAATAAATTTTTAT
5822083 AATTAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 3 0.08
29 16 0.43
30 12 0.32
31 6 0.16
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (29 bp):
AAATAAATTTTTATTCTTTTATTACAATC
Found at i:5823978 original size:67 final size:67
Alignment explanation
Indices: 5823890--5824023 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
5823880 TTAAATCCAG
5823890 AAAAGAAAAAAAAAATTGGTTGCCCATATAATTGTATGAGAGAAATGTCACCAGTAGAGATAAGT
1 AAAAGAAAAAAAAAATTGGTTGCCCATATAATTGTATGAGAGAAATGTCACCAGTAGAGATAAGT
5823955 CA
66 CA
*
5823957 AAAAG-AACAAAAAATTAGGTTGCCCATATAATTGTATGAGAGAAATGTCACCAGTAGAGATAAG
1 AAAAGAAAAAAAAAATT-GGTTGCCCATATAATTGTATGAGAGAAATGTCACCAGTAGAGATAAG
5824021 TCA
65 TCA
5824024 TACGAACGTA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 10 0.15
67 55 0.85
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (67 bp):
AAAAGAAAAAAAAAATTGGTTGCCCATATAATTGTATGAGAGAAATGTCACCAGTAGAGATAAGT
CA
Found at i:5826659 original size:2 final size:2
Alignment explanation
Indices: 5826652--5826699 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5826642 TGCATTAAAG
5826652 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5826694 TA TA TA
1 TA TA TA
5826700 AAAATATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5827130 original size:21 final size:19
Alignment explanation
Indices: 5827105--5827147 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
5827095 GGAATAAAAC
*
5827105 TTTTTAATTTATTGATTTATA
1 TTTTTAATTT-TAGATTT-TA
*
5827126 TTTTTAGTTTTAGATTTTA
1 TTTTTAATTTTAGATTTTA
5827145 TTT
1 TTT
5827148 AATCATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTTAATTTTAGATTTTA
Found at i:5828183 original size:10 final size:10
Alignment explanation
Indices: 5828153--5828186 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5828143 TCATTAAAAC
5828153 AAATATTTTA
1 AAATATTTTA
*
5828163 ATATAATTTTA
1 AAAT-ATTTTA
5828174 AAATATTTTA
1 AAATATTTTA
5828184 AAA
1 AAA
5828187 GTAAGTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATATTTTA
Found at i:5828202 original size:2 final size:2
Alignment explanation
Indices: 5828195--5828231 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5828185 AAGTAAGTTG
*
5828195 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5828232 CTTGCTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5841585 original size:15 final size:15
Alignment explanation
Indices: 5841474--5841616 Score: 58
Period size: 15 Copynumber: 9.0 Consensus size: 15
5841464 TATAAGTTTA
5841474 ATATACTTATATTTTT
1 ATATA-TTATATTTTT
*
5841490 -TATTGTTA-ATTTTT
1 ATA-TATTATATTTTT
*
5841504 ATATAATACTATCTTTT
1 ATATATTA-TAT-TTTT
* * * *
5841521 AAATATATTTTAATGTC
1 --ATATATTATATTTTT
*
5841538 ATATATTTTATTTTT
1 ATATATTATATTTTT
* * *
5841553 ATTTTATTATAATATT
1 A-TATATTATATTTTT
5841569 ATATATTATATTTTT
1 ATATATTATATTTTT
*
5841584 AT-TTTTAATATAATTTT
1 ATATATT-ATAT--TTTT
*
5841601 TTATATTATATATTTT
1 ATATATTATAT-TTTT
5841617 GTTTTAATTT
Statistics
Matches: 94, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
14 12 0.13
15 37 0.39
16 19 0.20
17 15 0.16
18 5 0.05
19 6 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (15 bp):
ATATATTATATTTTT
Found at i:5841596 original size:32 final size:32
Alignment explanation
Indices: 5841538--5841621 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
5841528 TTTTAATGTC
* *
5841538 ATATATTTTATTTTTA-TTTTATTATAATATT
1 ATATATTATATTTTTATTTTTAATATAATATT
*
5841569 ATATATTATATTTTTATTTTTAATATAATTTT
1 ATATATTATATTTTTATTTTTAATATAATATT
* *
5841601 TTATATTATATATTTTGTTTT
1 ATATATTATAT-TTTTATTTT
5841622 AATTTTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 15 0.33
32 23 0.50
33 8 0.17
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (32 bp):
ATATATTATATTTTTATTTTTAATATAATATT
Found at i:5841721 original size:22 final size:22
Alignment explanation
Indices: 5841691--5841737 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5841681 CTAATTCTTA
*
5841691 TATTATATTTTAGATTTTAA-AT
1 TATTATATTTTA-ATTATAATAT
*
5841713 TATTTTATTTTAATTATAATAT
1 TATTATATTTTAATTATAATAT
5841735 TAT
1 TAT
5841738 AAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTATATTTTAATTATAATAT
Found at i:5845486 original size:23 final size:23
Alignment explanation
Indices: 5845443--5845486 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5845433 TTCTTATCTT
* *
5845443 CTTCTTCTTTGTTTTTTTTTCAA
1 CTTCTTCTTTGTCTTTATTTCAA
5845466 CTTCTTCTTCT-TCTTTATTTC
1 CTTCTTCTT-TGTCTTTATTTC
5845487 TCTCTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.68
Consensus pattern (23 bp):
CTTCTTCTTTGTCTTTATTTCAA
Found at i:5846173 original size:38 final size:37
Alignment explanation
Indices: 5846120--5846193 Score: 130
Period size: 38 Copynumber: 2.0 Consensus size: 37
5846110 CCCCAAGGCC
5846120 TTTTTTTTTGGGTTATTTTATGTTGATTGGATTTAAT
1 TTTTTTTTTGGGTTATTTTATGTTGATTGGATTTAAT
*
5846157 TTTTTTGTTTGTGTTATTTTATGTTGATTGGATTTAA
1 TTTTTT-TTTGGGTTATTTTATGTTGATTGGATTTAA
5846194 GTTACTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 6 0.17
38 29 0.83
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (37 bp):
TTTTTTTTTGGGTTATTTTATGTTGATTGGATTTAAT
Found at i:5847830 original size:27 final size:27
Alignment explanation
Indices: 5847800--5847851 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5847790 TCGTTTTCTA
* *
5847800 CTCCGTCAACATCTTCCTCGTCCTCTT
1 CTCCGCCAACATCTTCCTCATCCTCTT
* *
5847827 CTCCGCCATCCTCTTCCTCATCCTC
1 CTCCGCCAACATCTTCCTCATCCTC
5847852 ATCCTCATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.10, C:0.50, G:0.06, T:0.35
Consensus pattern (27 bp):
CTCCGCCAACATCTTCCTCATCCTCTT
Found at i:5847850 original size:6 final size:6
Alignment explanation
Indices: 5847833--5847893 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
5847823 TCTTCTCCGC
* * * * * *
5847833 CATCCT CTTCCT CATCCT CATCCT CATCAT CATCAT CTTCAT CATCGT
1 CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT
5847881 CATCCT CATCCT C
1 CATCCT CATCCT C
5847894 TGGGTCTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.18, C:0.44, G:0.02, T:0.36
Consensus pattern (6 bp):
CATCCT
Found at i:5847868 original size:15 final size:15
Alignment explanation
Indices: 5847844--5847890 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5847834 ATCCTCTTCC
*
5847844 TCATCCTCATCCTCA
1 TCATCATCATCCTCA
*
5847859 TCATCATCATCTTCA
1 TCATCATCATCCTCA
*
5847874 TCATCGTCATCCTCA
1 TCATCATCATCCTCA
5847889 TC
1 TC
5847891 CTCTGGGTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.21, C:0.40, G:0.02, T:0.36
Consensus pattern (15 bp):
TCATCATCATCCTCA
Found at i:5856535 original size:2 final size:2
Alignment explanation
Indices: 5856501--5856600 Score: 129
Period size: 2 Copynumber: 52.5 Consensus size: 2
5856491 AACATACATA
* *
5856501 AT AT A- AT AT A- AT AT A- AT AT -T TT AT AT AT GT 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
* *
5856539 AT AT A- AT AT AT AT AC AT AT AN AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5856580 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
5856601 ATTTTATCCA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
1 5 0.06
2 81 0.94
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5872818 original size:16 final size:16
Alignment explanation
Indices: 5872797--5872827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5872787 TAAGAAATAA
*
5872797 TAAAAATAATTATTAT
1 TAAAAATAATCATTAT
5872813 TAAAAATAATCATTA
1 TAAAAATAATCATTA
5872828 AAAAGATTTG
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAATAATCATTAT
Found at i:5874156 original size:251 final size:250
Alignment explanation
Indices: 5873474--5875267 Score: 1838
Period size: 251 Copynumber: 7.2 Consensus size: 250
5873464 TAAGGTTAAT
* * * *
5873474 ATAACAAATTTAAAATTTTAACGTAATTGTGTGAGAGTTAATATAATAAA-TCAATTATGTAAAA
1 ATAACAAATTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAA-AAAGTCAATTATGTAAAA
** * * *
5873538 ATAATCTATTTTTAATGAAAAATAAATATTTAAA-TTATATTCTCAGATTAAAAATATTTAACGA
65 A-AAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAACGA
* ** *
5873602 TATATAAATTTTAATTTTAAAATAAAAAATAATACGGGTAAAAATAATTATAGTTAAAAGTTGTC
129 TATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCC
* * * *
5873667 ATT-AAAAAACTTTAAT-GTAAAACTGTCAA-AATGGACGTAAAAACTTATAAAAGTATA
194 ATTGAAAAATC-TTAATCATAAAA-TGT-AAGAATTGACGTAAAAACTTATAAAAGTAGA
* *
5873724 ATAA-ATAAGTTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAATTCAATTAAGTAAA
1 ATAACA-AA-TTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAAGTCAATTATGTAAA
* * * * * * * *
5873788 AAAAACTAATTTTAATGAAAAACAAACATTTAAATTCATATTCCCAAGTTAAAAGT-GTTAAAGA
64 AAAAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAACGA
* * * *
5873852 TATATGAATTTTAATTTTCAAATAAAGAGTAATAAGAATAAAAATAATTATAGTTTAAAA-TTGC
129 TATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAG-TTAAAAGTTGC
* * * * * * *
5873916 AATTGAAAAGTCTT-ATCATAGACATATAAGAATTGATGTAAAAACTTATAAATGTGGA
193 CATTGAAAAATCTTAATCATA-AAATGTAAGAATTGACGTAAAAACTTATAAAAGTAGA
* * * *
5873974 ATAATCAAATTTAAAATCTAAACATAAATATGTAAGAGTTAATGTAACAAGTCAATTATGTAAAA
1 ATAA-CAAATTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAAGTCAATTATGT-AAA
* * ** * *
5874039 AAAAAATATTTTTAATGAAAAATAAATATTTAAATTTATATTTTCGGACT-AAAGTATTTAATGA
64 AAAAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAACGA
*
5874103 TATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCT
129 TATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCC
* * * *
5874168 ATTAAAAAATTTTAAT-GTAAAACTGTAAGAATTGACATAAAAACTTATAAAAGTAGA
194 ATTGAAAAATCTTAATCATAAAA-TGTAAGAATTGACGTAAAAACTTATAAAAGTAGA
* * *
5874225 ATAAACAAATTTAAAATCTTAACATAAATGAT-TGAGAGTTAACGTAAAAAATCAATTAAGTAAA
1 AT-AACAAATTTAAAATCTTAACATAAATG-TGTGAGAGTTAATGTAAAAAGTCAATTATGTAAA
* * *
5874289 AAAAACTAATTTTAATGGAAAA-AAATA--TATATTTATATTCTCAAATTAAAAGTATTTAACGA
64 AAAAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAACGA
* * *
5874351 TATATAAATTTTAATTTTTAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTACC
129 TATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCC
* * *
5874416 ATTGAAAAATCTTAA-CATAAAACTGTAATAATTGA-GATAAAAACTTATAAATGTGGA
194 ATTGAAAAATCTTAATCATAAAA-TGTAAGAATTGACG-TAAAAACTTATAAAAGTAGA
* * * ** * *
5874473 ATCGAAAAAATTTTAAATCTT-AC-TGCAAATGTGTGAAAGTTAACATAAAAAGTTAATTAAGT-
1 AT--AACAAATTTAAAATCTTAACAT--AAATGTGTGAGAGTTAATGTAAAAAGTCAATTATGTA
* * * * * * *
5874535 -TAAAAAATAATTTTAATAAAAAATAAATATTTAAATTTATATTCTCCAAGTAAAATTTTTTAAT
62 AAAAAAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAAC
* * * * *
5874599 GATATATAATTTTTAATTTTTAAATAAAGAGTAATAAGAATAAAAATAATTATAATTAAAAGTTG
127 GATATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTG
* ** * **
5874664 CTATTGAAAAGCCTTGA-CATAAAAATGTAAGAATTGATATAAAAACTTAT-AAAGTTTA-A
192 CCATTGAAAAATCTTAATCAT-AAAATGTAAGAATTGACGTAAAAACTTATAAAAG--TAGA
* ** *
5874723 ATAACTAAATTTAAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTATGTAAAA
1 ATAAC-AAATTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAAGTCAATTATGTAAAA
* * * * *
5874788 AAATATATTTTTAATAAAAAACAAATATTTAAATTTATATTCTCATATTAAAAGTATTTAACGAT
65 AAAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAACGAT
*
5874853 ATATAAATTTTAATTTTAAAATAAAAAATAATAATAATAAAAATAATTATAGTTAAAAGTTGCCA
130 ATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCCA
* * * * *
5874918 TTAAAAAAATCTTAAT-GTAAAGTTGTAAAAATTAACGTAAAAACTTATAAAAGT-GAA
195 TT-GAAAAATCTTAATCATAAA-ATGTAAGAATTGACGTAAAAACTTATAAAAGTAG-A
* * * * *
5874975 ATAAACAAATTTAAAAT-TTCAAAATAAATATGTGAGAGTTAAAGTAAAAATTC-A--AT-TAAT
1 AT-AACAAATTTAAAATCTT-AACATAAATGTGTGAGAGTTAATGTAAAAAGTCAATTATGTAAA
* * * ** *
5875035 AAAAAATAATTTTAATGAAAAATTAAA-ATTTATATTTATATTATTGAGCTT-AAAGTATTTATC
64 AAAAAATAATTTTAATGAAAAA-TAAATATTTAAATTTATATT-CTCAAATTAAAAGTATTTAAC
* * *
5875098 GATATAT--A----AATTTT--AATAAAAAATAATAAGGATAAAAATAATTATAATTAAAAGTTA
127 GATATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTG
* * * * * *
5875155 CCATTGAAAAGTTTTGA-CGTAAAATCATAAGAATTGACGTAAAAATTTAT-AAAGATAGA
192 CCATTGAAAAATCTTAATCATAAAAT-GTAAGAATTGACGTAAAAACTTATAAAAG-TAGA
* *
5875214 ATAAACAAATTTAAAATCTTAACGTAAATGTGTGAGAGTTAATGTAATAAGTCA
1 AT-AACAAATTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAAGTCA
5875268 TAATGATAAT
Statistics
Matches: 1294, Mismatches: 197, Indels: 116
0.81 0.12 0.07
Matches are distributed among these distances:
238 5 0.00
239 79 0.06
240 47 0.04
242 6 0.00
246 1 0.00
247 35 0.03
248 188 0.15
249 112 0.09
250 338 0.26
251 400 0.31
252 76 0.06
253 7 0.01
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.34
Consensus pattern (250 bp):
ATAACAAATTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAAGTCAATTATGTAAAAA
AAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTCAAATTAAAAGTATTTAACGATA
TATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCCAT
TGAAAAATCTTAATCATAAAATGTAAGAATTGACGTAAAAACTTATAAAAGTAGA
Found at i:5874541 original size:501 final size:491
Alignment explanation
Indices: 5873474--5875260 Score: 1902
Period size: 501 Copynumber: 3.6 Consensus size: 491
5873464 TAAGGTTAAT
* * * * * *
5873474 ATAACAAATTTAAAATTTTAACGTAATTGTGTGAGAGTTAATATAATAAATCAATTATGTAAAAA
1 ATAAAAAATTTAAAATCTT-AC-TAAATATGTGAAAGTTAATATAA-AAATCAATTAAGT-AAAA
* * * *
5873539 TAATCTATTTTTAATGAAAAATAAATATTTAAA-TTATATTCTCAGATTAAAAATATTTAACGAT
62 -AA--TAATTTTAATGAAAAATAAATATTTAAATTTATATTCTC-GACTAAAAGTATTTAATGAT
* ** *
5873603 ATATAAATTTTAATTTTAAAATAAAAAATAATACGGGTAAAAATAATTATAGTTAAAAGTTG-TC
123 ATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAATTAAAAGTTGCT-
* * * * *
5873667 ATTAAAAAACTTTAATGTAAAACTGTCAA-AATGGACGTAAAAACTTATAAAAG-TATAATAAAT
187 ATTAAAAAACTTTAACGTAAAACTGT-AAGAATTGACATAAAAACTTAT-AAAGTTAGAATAAAC
* * *
5873730 AAGTTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAATTCAATTAAGTAAAAAAAACT
250 AAATTTAAAATCTTAACATAAATGTGTGAGAGTTAACGTAAAAAATCAATTAAGTAAAAAAAACT
* * * * * * *
5873795 AATTTTAATGAAAAACAAACATTTAAATTCATATTCCCAAGTTAAAAGT-GTTAAAGATATATGA
315 AATTTTAATG-AAAA-AAA-ATATAAATTTATATTCTCAAATTAAAAGTATTTAACGATATATAA
* * * * *
5873859 ATTTTAATTTTCAAATAAAGAGTAATAAGAATAAAAATAATTATAGTTTAAAATTGCAATTGAAA
377 ATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTGCCATTGAAA
* * * * * *
5873924 AGTCTTATCAT-AGACATATAAGAATTGATGTAAAAACTTATAAATGTGGA
442 AATCTTAACATAAAAC-TGTAAAAATTGACGTAAAAACTTATAAATGTGGA
* * * * *
5873974 ATAATCAAATTTAAAATCTAAACATAAATATGT-AAGAGTTAATGTAACAAGTCAATTATGTAAA
1 ATAA-AAAATTTAAAATCT-TAC-TAAATATGTGAA-AGTTAATATAA-AAATCAATTAAGT---
* *
5874038 AAAAAAATATTTTTAATGAAAAATAAATATTTAAATTTATATTTTCGGACT-AAAGTATTTAATG
58 -AAAAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCTC-GACTAAAAGTATTTAATG
*
5874102 ATATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGC
121 ATATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAATTAAAAGTTGC
* *
5874167 TATTAAAAAATTTTAATGTAAAACTGTAAGAATTGACATAAAAACTTATAAAAG-TAGAATAAAC
186 TATTAAAAAACTTTAACGTAAAACTGTAAGAATTGACATAAAAACTTAT-AAAGTTAGAATAAAC
5874231 AAATTTAAAATCTTAACATAAATGAT-TGAGAGTTAACGTAAAAAATCAATTAAGTAAAAAAAAC
250 AAATTTAAAATCTTAACATAAATG-TGTGAGAGTTAACGTAAAAAATCAATTAAGTAAAAAAAAC
* *
5874295 TAATTTTAATGGAAAAAAATATATATTTATATTCTCAAATTAAAAGTATTTAACGATATATAAAT
314 TAATTTTAATGAAAAAAAATATAAATTTATATTCTCAAATTAAAAGTATTTAACGATATATAAAT
* *
5874360 TTTAATTTTTAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTACCATTGAAAAA
379 TTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTGCCATTGAAAAA
*
5874425 TCTTAACATAAAACTGTAATAATTGA-GATAAAAACTTATAAATGTGGA
444 TCTTAACATAAAACTGTAAAAATTGACG-TAAAAACTTATAAATGTGGA
* * * *
5874473 ATCGAAAAAATTTTAAATCTTACTGCAAATGTGTGAAAGTTAACATAAAAAGTTAATTAAGTTAA
1 AT--AAAAAATTTAAAATCTTACT--AAATATGTGAAAGTTAATATAAAAA-TCAATTAAG-TAA
* * * * *
5874538 AAAATAATTTTAATAAAAAATAAATATTTAAATTTATATTCTCCAAGTAAAATTTTTTAATGATA
60 AAAATAATTTTAATGAAAAATAAATATTTAAATTTATATTCT-CGACTAAAAGTATTTAATGATA
* * * *
5874603 TATAATTTTTAATTTTTAAATAAAGAGTAATAAGAATAAAAATAATTATAATTAAAAGTTGCTAT
124 TATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAATTAAAAGTTGCTAT
* * * * * * *
5874668 TGAAAAGCCTTGACATAAAAATGTAAGAATTGATATAAAAACTTATAAAGTTTA-AAT-AACTAA
189 TAAAAAACTTTAACGTAAAACTGTAAGAATTGACATAAAAACTTATAAAG-TTAGAATAAAC-AA
* * * * *
5874731 ATTTAAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTATGTAAAAAAATA-TA
252 ATTTAAAATCTTAACATAAATGTGTGAGAGTTAACGTAAAAAATCAATTAAGTAAAAAAA-ACTA
* * *
5874795 TTTTTAATAAAAAACAAATATTTAAATTTATATTCTCATATTAAAAGTATTTAACGATATATAAA
316 ATTTTAATGAAAAA-AAATA--TAAATTTATATTCTCAAATTAAAAGTATTTAACGATATATAAA
* * *
5874860 TTTTAATTTTAAAATAAAAAATAATAATAATAAAAATAATTATAGTTAAAAGTTGCCATTAAAAA
378 TTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTGCCATT-GAAA
** ** * * *
5874925 AATCTTAATGTAAAGTTGTAAAAATTAACGTAAAAACTTATAAAAGTGAA
442 AATCTTAACATAAAACTGTAAAAATTGACGTAAAAACTTATAAATGTGGA
* *
5874975 ATAAACAAATTTAAAAT-TTCAAAATAAATATGTGAGAGTTAA-AGTAAAAATTCAATTAA-TAA
1 ATAAA-AAATTTAAAATCTT---ACTAAATATGTGAAAGTTAATA-TAAAAA-TCAATTAAGTAA
* * * *
5875037 AAAATAATTTTAATGAAAAATTAAA-ATTTATATTTATATTATTGAGCTTAAAGTATTT-ATCGA
60 AAAATAATTTTAATGAAAAA-TAAATATTTAAATTTATATTCTCGA-CTAAAAGTATTTAAT-GA
* * *
5875100 TATAT--A----AATTTT--AATAAAAAATAATAAGGATAAAAATAATTATAATTAAAAGTTACC
122 TATATAAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAATTAAAAGTTGCT
* ** * * * * *
5875157 ATTGAAAAGTTTTGACGTAAAA-TCATAAGAATTGACGTAAAAATTTATAAAGATAGAATAAACA
187 ATTAAAAAACTTTAACGTAAAACT-GTAAGAATTGACATAAAAACTTATAAAGTTAGAATAAACA
* *
5875221 AATTTAAAATCTTAACGTAAATGTGTGAGAGTTAATGTAA
251 AATTTAAAATCTTAACATAAATGTGTGAGAGTTAACGTAA
5875261 TAAGTCATAA
Statistics
Matches: 1115, Mismatches: 129, Indels: 95
0.83 0.10 0.07
Matches are distributed among these distances:
490 3 0.00
491 125 0.11
492 3 0.00
493 6 0.01
497 51 0.05
498 212 0.19
499 179 0.16
500 58 0.05
501 409 0.37
502 59 0.05
503 5 0.00
504 5 0.00
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.34
Consensus pattern (491 bp):
ATAAAAAATTTAAAATCTTACTAAATATGTGAAAGTTAATATAAAAATCAATTAAGTAAAAAATA
ATTTTAATGAAAAATAAATATTTAAATTTATATTCTCGACTAAAAGTATTTAATGATATATAAAT
TTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAATTAAAAGTTGCTATTAAAAAA
CTTTAACGTAAAACTGTAAGAATTGACATAAAAACTTATAAAGTTAGAATAAACAAATTTAAAAT
CTTAACATAAATGTGTGAGAGTTAACGTAAAAAATCAATTAAGTAAAAAAAACTAATTTTAATGA
AAAAAAATATAAATTTATATTCTCAAATTAAAAGTATTTAACGATATATAAATTTTAATTTTAAA
ATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTGCCATTGAAAAATCTTAACATAAA
ACTGTAAAAATTGACGTAAAAACTTATAAATGTGGA
Found at i:5875040 original size:749 final size:747
Alignment explanation
Indices: 5873471--5875255 Score: 2184
Period size: 749 Copynumber: 2.4 Consensus size: 747
5873461 TTCTAAGGTT
* * * *
5873471 AATATAACAAATTTAAAATTTTAACGTAATTGTGTGAGAGTTAATA-TAATAAATCAATTATGTA
1 AATA-AACAAATTTAAAA-TTTAACATAAATATGTGAGAGTTAA-AGTAA-AAATCAATTA-ATA
* * * * *
5873535 AAAATAATCTATTTTTAATGAAAAATAAATATTTAAATTATATTCTCAGATTAAAAATATTTAAC
61 AAAA-AAACTAATTTTAATGAAAAA-AAATATAT-ATTTATATTCTCAGATTAAAAGTATTTAAC
* * * *
5873600 GATATATAAATTTTAATTTTAAAATAAAAAATAATACGGGTAAAAATAATTATAGTTAAAAGTTG
123 GATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAATTATAGTTAAAAGTTA
* ** *
5873665 TCATT-AAAAAACTTTAATGTAAAACTGTCAAAATGGACGTAAAAACTTATAAAAGTATAATAAA
188 CCATTGAAAAAACTTTAACATAAAACTGTCAAAATGGACGTAAAAACTTATAAAAGTAGAATAAA
* * **
5873729 TAAGTTTAAAATCTTAACATAAATGTGTGAGAGTTAATGTAAAAATTCAATTAAGTAAAAAAAAC
253 TAAATTTAAAATCTTAACATAAATGTGTGAAAGTTAACATAAAAATTCAATTAAGTAAAAAAAAC
*
5873794 TAATTTTAATGAAAAACAAACATTTAAATTCATATTCCCAAGTTAAAAGTGTTAAAGATATATGA
318 TAATTTTAATAAAAAACAAACATTTAAATTCATATTCCCAAGTTAAAAGTGTTAAAGATATATGA
*
5873859 ATTTTAATTTTCAAATAAAGAGTAATAAGAATAAAAATAATTATAGTTTAAAATTGCAATTGAAA
383 ATTTTAATTTTCAAATAAAGAGTAATAAGAATAAAAATAATTATAGATTAAAATTGCAATTGAAA
* * * * *
5873924 AGTCTTATCATAGACATATAAGAATTGATGTAAAAACTTATAAATGTGGAATAATCAAATTTAAA
448 AGCCTTATCATAAAAATATAAGAATTGATATAAAAACTTATAAATGTGAAATAATCAAATTTAAA
**
5873989 ATCTAAACATAAATATGTAAGAGTTAATGTAACAAGTCAATTATGTAAAAAAAAAATATTTTTAA
513 ATCTAAACATAAATATGTAAGAGTTAACATAACAAGTCAATTATGTAAAAAAAAAATATTTTTAA
* * * * *
5874054 TGAAAAATAAATATTTAAATTTATATTTTCGGACTAAAGTATTTAATGATATATAAATTTTAATT
578 TAAAAAACAAATATTTAAATTTATATTCTCAGACTAAAGTATTTAACGATATATAAATTTTAATT
* *
5874119 TTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCTATTAAAAAATTTTAAT
643 TTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCCATTAAAAAATCTTAAT
* *
5874184 GTAAAACTGTAAGAATTGACATAAAAACTTATAAAAGTAG
708 GTAAAACTGTAAAAATTAACATAAAAACTTATAAAAGTAG
*
5874224 AATAAACAAATTTAAAATCTTAACATAAATGAT-TGAGAGTTAACGTAAAAAATCAATTAAGTAA
1 AATAAACAAATTTAAAAT-TTAACATAAAT-ATGTGAGAGTTAAAGT-AAAAATCAATTAA-TAA
* *
5874288 AAAAAACTAATTTTAATGGAAAAAAATATATATTTATATTCTCAAATTAAAAGTATTTAACGATA
62 AAAAAACTAATTTTAATGAAAAAAAATATATATTTATATTCTCAGATTAAAAGTATTTAACGATA
* *
5874353 TATAAATTTTAATTTTTAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAATTACCAT
127 TATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAATTATAGTTAAAAGTTACCAT
* * * *
5874418 TGAAAAATC-TTAACATAAAACTGT-AATAATTGA-GATAAAAACTTATAAATGTGGAATCGAAA
192 TGAAAAAACTTTAACATAAAACTGTCAA-AATGGACG-TAAAAACTTATAAAAGTAGAAT--AAA
* *
5874480 -AAATTTTAAATCTT-AC-TGCAAATGTGTGAAAGTTAACATAAAAAGTT-AATTAAGT-TAAAA
253 TAAATTTAAAATCTTAACAT--AAATGTGTGAAAGTTAACATAAAAA-TTCAATTAAGTAAAAAA
* * * * * *
5874540 AA-TAATTTTAATAAAAAATAAATATTTAAATTTATATTCTCCAAG-TAAAATTTTTTAATGATA
315 AACTAATTTTAATAAAAAACAAACATTTAAATTCATATTC-CCAAGTTAAAA-GTGTTAAAGATA
* *
5874603 TAT-AATTTTTAATTTTTAAATAAAGAGTAATAAGAATAAAAATAATTATA-ATTAAAAGTTGCT
378 TATGAA-TTTTAATTTTCAAATAAAGAGTAATAAGAATAAAAATAATTATAGATTAAAA-TTGCA
* *
5874666 ATTGAAAAGCCTTGA-CATAAAAATGTAAGAATTGATATAAAAACTTATAAA-GTTTAAATAA-C
441 ATTGAAAAGCCTT-ATCATAAAAATATAAGAATTGATATAAAAACTTATAAATG-TGAAATAATC
* * * * *
5874728 TAAATTTAAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTATGT-AAAAAAAT
504 -AAATTTAAAATCTAAACATAAATATGTAAGAGTTAACATAACAAGTCAATTATGTAAAAAAAAA
* *
5874792 ATATTTTTAATAAAAAACAAATATTTAAATTTATATTCTCATATTAAAAGTATTTAACGATATAT
568 ATATTTTTAATAAAAAACAAATATTTAAATTTATATTCTCAGACT-AAAGTATTTAACGATATAT
*
5874857 AAATTTTAATTTTAAAATAAAAAATAATAATAATAAAAATAATTATAGTTAAAAGTTGCCATTAA
632 AAATTTTAATTTTAAAATAAAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCCATT-A
** *
5874922 AAAAATCTTAATGTAAAGTTGTAAAAATTAACGTAAAAACTTATAAAAGT-G
696 AAAAATCTTAATGTAAAACTGTAAAAATTAACATAAAAACTTATAAAAGTAG
*
5874973 AAATAAACAAATTTAAAATTTCAAAATAAATATGTGAGAGTTAAAGTAAAAATTCAATTAAT--A
1 -AATAAACAAATTTAAAATTT-AACATAAATATGTGAGAGTTAAAGTAAAAA-TCAATTAATAAA
* * * * *
5875036 AAAAA-TAATTTTAATGAAAAATTAAAATTTATATTTATATTATTGAGCTT-AAAGTATTTATCG
63 AAAAACTAATTTTAATG-AAAA--AAAATATATATTTATATT-CTCAGATTAAAAGTATTTAACG
*
5875099 ATATAT--A----AA-TTTT-AATAAAAAATAATAAGGATAAAAATAATTATAATTAAAAGTTAC
124 ATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAATTATAGTTAAAAGTTAC
** * * * * *
5875156 CATTG-AAAAGTTTTGACGTAAAA-TCAT-AAGAATTGACGTAAAAATTTAT-AAAGATAGAATA
189 CATTGAAAAAACTTTAACATAAAACT-GTCAA-AATGGACGTAAAAACTTATAAAAG-TAGAATA
* * *
5875217 AACAAATTTAAAATCTTAACGTAAATGTGTGAGAGTTAA
251 AATAAATTTAAAATCTTAACATAAATGTGTGAAAGTTAA
5875256 TGTAATAAGT
Statistics
Matches: 901, Mismatches: 94, Indels: 87
0.83 0.09 0.08
Matches are distributed among these distances:
739 3 0.00
740 37 0.04
741 81 0.09
742 6 0.01
743 2 0.00
746 11 0.01
747 10 0.01
748 98 0.11
749 423 0.47
750 151 0.17
751 23 0.03
752 49 0.05
753 7 0.01
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.34
Consensus pattern (747 bp):
AATAAACAAATTTAAAATTTAACATAAATATGTGAGAGTTAAAGTAAAAATCAATTAATAAAAAA
AACTAATTTTAATGAAAAAAAATATATATTTATATTCTCAGATTAAAAGTATTTAACGATATATA
AATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAATTATAGTTAAAAGTTACCATTGAA
AAAACTTTAACATAAAACTGTCAAAATGGACGTAAAAACTTATAAAAGTAGAATAAATAAATTTA
AAATCTTAACATAAATGTGTGAAAGTTAACATAAAAATTCAATTAAGTAAAAAAAACTAATTTTA
ATAAAAAACAAACATTTAAATTCATATTCCCAAGTTAAAAGTGTTAAAGATATATGAATTTTAAT
TTTCAAATAAAGAGTAATAAGAATAAAAATAATTATAGATTAAAATTGCAATTGAAAAGCCTTAT
CATAAAAATATAAGAATTGATATAAAAACTTATAAATGTGAAATAATCAAATTTAAAATCTAAAC
ATAAATATGTAAGAGTTAACATAACAAGTCAATTATGTAAAAAAAAAATATTTTTAATAAAAAAC
AAATATTTAAATTTATATTCTCAGACTAAAGTATTTAACGATATATAAATTTTAATTTTAAAATA
AAAAATAATAAGAATAAAAATAATTATAGTTAAAAGTTGCCATTAAAAAATCTTAATGTAAAACT
GTAAAAATTAACATAAAAACTTATAAAAGTAG
Found at i:5875375 original size:17 final size:16
Alignment explanation
Indices: 5875348--5875391 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
5875338 TTTAAGCTAA
5875348 AAAATAGAATAAAATTT
1 AAAATA-AATAAAATTT
*
5875365 AAAATCAAATAACATTT
1 AAAAT-AAATAAAATTT
5875382 AAAATAAATA
1 AAAATAAATA
5875392 GATGTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 19 0.76
18 1 0.04
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAATAAATAAAATTT
Found at i:5898893 original size:29 final size:29
Alignment explanation
Indices: 5898848--5898941 Score: 116
Period size: 29 Copynumber: 3.1 Consensus size: 29
5898838 TTAACTATGC
5898848 AATAAGATAAAAGGACATAATCAATAAAA
1 AATAAGATAAAAGGACATAATCAATAAAA
* *
5898877 AATAAGATAAAAAGACATAATCATTAAAAAAA
1 AATAAGATAAAAGGACATAATC---AATAAAA
*
5898909 GTAATAAGATAAAAGGACATAATCATTAAAA
1 --AATAAGATAAAAGGACATAATCAATAAAA
5898940 AA
1 AA
5898942 AATTCTTATG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 23 0.42
31 5 0.09
32 6 0.11
34 21 0.38
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (29 bp):
AATAAGATAAAAGGACATAATCAATAAAA
Found at i:5898920 original size:34 final size:32
Alignment explanation
Indices: 5898848--5898943 Score: 135
Period size: 34 Copynumber: 3.0 Consensus size: 32
5898838 TTAACTATGC
*
5898848 AATAAGATAAAAGGACATAATC---AATAAAA
1 AATAAGATAAAAGGACATAATCATTAAAAAAA
*
5898877 AATAAGATAAAAAGACATAATCATTAAAAAAA
1 AATAAGATAAAAGGACATAATCATTAAAAAAA
5898909 GTAATAAGATAAAAGGACATAATCATTAAAAAAA
1 --AATAAGATAAAAGGACATAATCATTAAAAAAA
5898943 A
1 A
5898944 TTCTTATGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
29 21 0.36
32 7 0.12
34 31 0.53
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (32 bp):
AATAAGATAAAAGGACATAATCATTAAAAAAA
Found at i:5900094 original size:15 final size:15
Alignment explanation
Indices: 5900074--5900113 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
5900064 ACATTATAAG
5900074 TAATGTAATTTTAGA
1 TAATGTAATTTTAGA
5900089 TAATGTAATTTTAGA
1 TAATGTAATTTTAGA
* *
5900104 GAATTTAATT
1 TAATGTAATT
5900114 GTATGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (15 bp):
TAATGTAATTTTAGA
Found at i:5901727 original size:3 final size:3
Alignment explanation
Indices: 5901713--5901743 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5901703 TGCACACTTC
*
5901713 AGA AGA ATA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5901744 ACATGATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:5902375 original size:14 final size:14
Alignment explanation
Indices: 5902356--5902385 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5902346 GTTTGGTAAA
*
5902356 TTTTTTTTTATAAG
1 TTTTTTTATATAAG
5902370 TTTTTTTATATAAG
1 TTTTTTTATATAAG
5902384 TT
1 TT
5902386 ATAATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTTTTATATAAG
Found at i:5902973 original size:15 final size:16
Alignment explanation
Indices: 5902951--5902984 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5902941 AAATCATCTT
*
5902951 CCATTTTCTCAACTTC
1 CCATTTCCTCAACTTC
*
5902967 CCATTTCCTCAATTTC
1 CCATTTCCTCAACTTC
5902983 CC
1 CC
5902985 CTTAAAACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (16 bp):
CCATTTCCTCAACTTC
Found at i:5931310 original size:21 final size:21
Alignment explanation
Indices: 5931286--5931327 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5931276 AATGTAAAAA
*
5931286 ATGTCACATTA-TCATATTATG
1 ATGTCAAATTAGT-ATATTATG
5931307 ATGTCAAATTAGTATATTATG
1 ATGTCAAATTAGTATATTATG
5931328 TTATTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTCAAATTAGTATATTATG
Found at i:5931395 original size:33 final size:32
Alignment explanation
Indices: 5931324--5931402 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
5931314 ATTAGTATAT
* * *
5931324 TATGTTATTATCAATTATGATATATCAACATG
1 TATGTCATTATCAATTATAATATATCAACATC
* *
5931356 TCATGTCATTATCAATTATAATATGTTAACATAC
1 T-ATGTCATTATCAATTATAATATATCAACAT-C
*
5931390 TATGTCAGTATCA
1 TATGTCATTATCA
5931403 TATGATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
32 1 0.03
33 37 0.95
34 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (32 bp):
TATGTCATTATCAATTATAATATATCAACATC
Found at i:5931484 original size:30 final size:30
Alignment explanation
Indices: 5931450--5931508 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5931440 CAATCATTAA
5931450 TTATTTGATTCAAAATAAAAATATAAAAAT
1 TTATTTGATTCAAAATAAAAATATAAAAAT
* *
5931480 TTATTTGATTCCAAATAAATATATAAAAA
1 TTATTTGATTCAAAATAAAAATATAAAAA
5931509 GTAATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (30 bp):
TTATTTGATTCAAAATAAAAATATAAAAAT
Found at i:5951793 original size:42 final size:42
Alignment explanation
Indices: 5951732--5951820 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
5951722 AATTAGGGCA
5951732 TTTACAGGGACTTGATTGGACTTACAAGCCTCCATTTTTCAG
1 TTTACAGGGACTTGATTGGACTTACAAGCCTCCATTTTTCAG
*
5951774 TTTACAGGGACTTGGTTGGACTTACAAGCCTCCATTTTTCAG
1 TTTACAGGGACTTGATTGGACTTACAAGCCTCCATTTTTCAG
5951816 TTTAC
1 TTTAC
5951821 CAGCTTACAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (42 bp):
TTTACAGGGACTTGATTGGACTTACAAGCCTCCATTTTTCAG
Found at i:5960589 original size:27 final size:28
Alignment explanation
Indices: 5960542--5960599 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
5960532 TAATTTATGT
5960542 AAAAATAATATTATTCATTTTAT-TTTA
1 AAAAATAATATTATTCATTTTATATTTA
* * *
5960569 AAAAATAATTTTCTTACTTTTTATATTTA
1 AAAAATAATATTATT-CATTTTATATTTA
5960598 AA
1 AA
5960600 CGCATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.50
28 7 0.27
29 6 0.23
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
AAAAATAATATTATTCATTTTATATTTA
Found at i:5963487 original size:15 final size:15
Alignment explanation
Indices: 5963467--5963523 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
5963457 TTTACAATAC
*
5963467 AATGTGATTATAGAT
1 AATGTGATTATAAAT
*
5963482 AATGTGATTGTAAAT
1 AATGTGATTATAAAT
* *
5963497 AATGTGACTGTAAAT
1 AATGTGATTATAAAT
*
5963512 AATGTAATTATA
1 AATGTGATTATA
5963524 GGAAAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.39
Consensus pattern (15 bp):
AATGTGATTATAAAT
Found at i:5963776 original size:33 final size:32
Alignment explanation
Indices: 5963739--5963825 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 32
5963729 TTTTAATATC
*
5963739 ATATATTTTATTTTTATTTTTTATTATAATCTT
1 ATATATTTTATTTTTATTTTTTAATATAAT-TT
*
5963772 ATATATTTTATTTTCACTTTTTTAATATAATTT
1 ATATATTTTATTTTTA-TTTTTTAATATAATTT
* *
5963805 TTATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
5963826 AATATTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTTTTAATATAATTT
Found at i:5963824 original size:20 final size:20
Alignment explanation
Indices: 5963757--5963841 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
5963747 TATTTTTATT
* *
5963757 TTTTATTATAATCTTATATA
1 TTTTATTTTAATATTATATA
* * *
5963777 TTTTATTTTCACTTTTTTA-A
1 TTTTATTTT-AATATTATATA
* * *
5963797 TATAATTTTTATATTATATA
1 TTTTATTTTAATATTATATA
* *
5963817 TTTTATTTTAATATTTTTTA
1 TTTTATTTTAATATTATATA
5963837 TTTTA
1 TTTTA
5963842 ATTATAACGT
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
19 5 0.10
20 37 0.77
21 6 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTTTAATATTATATA
Found at i:5963830 original size:15 final size:15
Alignment explanation
Indices: 5963791--5963843 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
5963781 ATTTTCACTT
5963791 TTTTAATATAATTTTTA
1 TTTTAATAT-A-TTTTA
*
5963808 TATT-ATATATTTTA
1 TTTTAATATATTTTA
*
5963822 TTTTAATATTTTTTA
1 TTTTAATATATTTTA
5963837 TTTTAAT
1 TTTTAAT
5963844 TATAACGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 8 0.25
15 17 0.53
16 4 0.12
17 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTAATATATTTTA
Found at i:5964932 original size:23 final size:24
Alignment explanation
Indices: 5964879--5964933 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
5964869 ATTCGTCTGC
*
5964879 TATGCTTTTGATTTTTCTTTCTCT
1 TATGTTTTTGATTTTTCTTTCTCT
*
5964903 TACGTTTTTAGATTTTTC-TT-TCT
1 TATGTTTTT-GATTTTTCTTTCTCT
5964926 TATGTTTT
1 TATGTTTT
5964934 GAAGATACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 9 0.33
25 8 0.30
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (24 bp):
TATGTTTTTGATTTTTCTTTCTCT
Found at i:5966120 original size:34 final size:31
Alignment explanation
Indices: 5966069--5966139 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
5966059 GTATATGAAA
* *
5966069 TGTAACAATAATATTTTTTTTCAACATGGCG
1 TGTAACAACAATATTTTTTTTCAACATGACG
5966100 TGTAACAACAATATTTTTTTTCAACATGACG
1 TGTAACAACAATATTTTTTTTCAACATGACG
5966131 TGTAACAAC
1 TGTAACAAC
5966140 CTAACTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (31 bp):
TGTAACAACAATATTTTTTTTCAACATGACG
Found at i:5979444 original size:30 final size:29
Alignment explanation
Indices: 5979379--5979455 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
5979369 TAAAATAATT
* * * *
5979379 TTTTATATTTTTATTATGTTTAATTAAAT
1 TTTTATATTTTTATTTTGTTCAAATAAAC
*
5979408 TTTTATATTTTTATTTTGTATCAAATAAGC
1 TTTTATATTTTTATTTTGT-TCAAATAAAC
5979438 TTTTATATTTTTATTTTG
1 TTTTATATTTTTATTTTG
5979456 AATTAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (29 bp):
TTTTATATTTTTATTTTGTTCAAATAAAC
Found at i:5979464 original size:29 final size:28
Alignment explanation
Indices: 5979379--5979465 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 28
5979369 TAAAATAATT
* * *
5979379 TTTTATATTTTTATTATGTTTAATTAAAT
1 TTTTATATTTTTATTTTGATTAA-TAAAC
* *
5979408 TTTTATATTTTTATTTTGTATCAAATAAGC
1 TTTTATATTTTTATTTTG-AT-TAATAAAC
5979438 TTTTATATTTTTATTTTGAATTAATAAA
1 TTTTATATTTTTATTTTG-ATTAATAAA
5979466 TTCTTATGAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 22 0.46
30 24 0.50
31 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTATATTTTTATTTTGATTAATAAAC
Found at i:5979472 original size:29 final size:28
Alignment explanation
Indices: 5979372--5979472 Score: 103
Period size: 29 Copynumber: 3.5 Consensus size: 28
5979362 AAAAAATTAA
* * *
5979372 AATAATTTTTTATATTTTTATTATGTTT
1 AATAAATTTTTATATTTTTATTTTGATT
*
5979400 AATTAAATTTTTATATTTTTATTTTGTATCA
1 AA-TAAATTTTTATATTTTTATTTTG-AT-T
**
5979431 AATAAGCTTTTATATTTTTATTTTGAATT
1 AATAAATTTTTATATTTTTATTTTG-ATT
*
5979460 AATAAATTCTTAT
1 AATAAATTTTTAT
5979473 GAGTAATTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
28 2 0.03
29 31 0.53
30 24 0.41
31 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (28 bp):
AATAAATTTTTATATTTTTATTTTGATT
Found at i:5980959 original size:2 final size:2
Alignment explanation
Indices: 5980952--5981001 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5980942 AACTTTAAAC
5980952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5980994 AT AT AT AT
1 AT AT AT AT
5981002 TTAATGGGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5984422 original size:15 final size:15
Alignment explanation
Indices: 5984402--5984432 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5984392 ACTTTACAAT
5984402 GTAATGTGATTACAG
1 GTAATGTGATTACAG
*
5984417 GTAATGTGATTGCAG
1 GTAATGTGATTACAG
5984432 G
1 G
5984433 AAAAATAATA
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:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (15 bp):
GTAATGTGATTACAG
Found at i:5984687 original size:33 final size:31
Alignment explanation
Indices: 5984649--5984731 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 31
5984639 TAATGTCATA
*
5984649 TATTTTATTTTTATTTCTTACTATAATCTTATT
1 TATTTTATTTTTATTTCTTAATATAAT-TT-TT
*
5984682 TATTTTATTTTTATTTTTTAATATAATTTTT
1 TATTTTATTTTTATTTCTTAATATAATTTTT
5984713 TATATTATATATTTTATTT
1 TAT-TT-TAT-TTTTATTT
5984732 TTATTTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
31 5 0.11
32 4 0.09
33 28 0.62
34 8 0.18
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (31 bp):
TATTTTATTTTTATTTCTTAATATAATTTTT
Found at i:5984703 original size:28 final size:29
Alignment explanation
Indices: 5984635--5984700 Score: 69
Period size: 33 Copynumber: 2.1 Consensus size: 29
5984625 CTTAAATATA
*
5984635 TTTTTAATGTCATATATTTTATTTTTATT
1 TTTTTAATCTCATATATTTTATTTTTATT
* *
5984664 TCTTACTATAATCTTATTTATTTTATTTTTATT
1 T-TT--T-TAATCTCATATATTTTATTTTTATT
5984697 TTTT
1 TTTT
5984701 AATATAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
29 1 0.03
30 3 0.10
32 3 0.10
33 23 0.77
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTTAATCTCATATATTTTATTTTTATT
Found at i:5984743 original size:55 final size:53
Alignment explanation
Indices: 5984677--5984803 Score: 123
Period size: 55 Copynumber: 2.3 Consensus size: 53
5984667 TACTATAATC
* * *
5984677 TTATTTATTTTATTTTTATT-TTTTAA-TATAATTTTTTATATTATATATTTTATTT
1 TTATTT-TTTTATTTTTATTATATAAATTATAATTTCTTATATT-T-TATTTTA-TT
** * *
5984732 TTATTTCTTTTACCTATATTATATAAATTTTAATTTCTTATATTTTATTTTATT
1 TTATTT-TTTTATTTTTATTATATAAATTATAATTTCTTATATTTTATTTTATT
*
5984786 TTAATTTTTTATTTTTAT
1 TTATTTTTTTATTTTTAT
5984804 ATTATATATT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
53 9 0.16
54 7 0.12
55 23 0.40
56 5 0.09
57 14 0.24
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (53 bp):
TTATTTTTTTATTTTTATTATATAAATTATAATTTCTTATATTTTATTTTATT
Found at i:5984743 original size:88 final size:88
Alignment explanation
Indices: 5984673--5984912 Score: 310
Period size: 88 Copynumber: 2.8 Consensus size: 88
5984663 TTCTTACTAT
* *
5984673 AATCTT-ATTTATTTTATTTT-TATT-TTTTAATATAAT-TTTTTATATTATATATTTTATTTTT
1 AATCTTAATTTATTATATTTTATATTATTTTAATATAATATTTTTATATTATATATTTTATTTTA
5984734 ATTTCTTTTACCTATATTATATA
66 ATTTCTTTTACCTATATTATATA
* * * * **
5984757 AATTTTAATTTCTTATATTTTATTTTATTTTAATTTTTTATTTTTATATTATATATTTTATTTTA
1 AATCTTAATTTATTATATTTTATATTATTTTAATATAATATTTTTATATTATATATTTTATTTTA
5984822 ATTTCTTTTACCTATATTATATA
66 ATTTCTTTTACCTATATTATATA
* * * ** *
5984845 AATTTTAATTTCTTATATTTTATTTTATTTTAAT-TTTTGATTTTTATATTATATGTTTTATTTT
1 AATCTTAATTTATTATATTTTATATTATTTTAATATAAT-ATTTTTATATTATATATTTTATTTT
5984909 AATT
65 AATT
5984913 ATAATGCTAC
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
84 5 0.04
85 12 0.08
86 3 0.02
87 13 0.09
88 109 0.77
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.68
Consensus pattern (88 bp):
AATCTTAATTTATTATATTTTATATTATTTTAATATAATATTTTTATATTATATATTTTATTTTA
ATTTCTTTTACCTATATTATATA
Found at i:5984788 original size:25 final size:24
Alignment explanation
Indices: 5984758--5984808 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
5984748 TATTATATAA
*
5984758 ATTTTAATTTCTTATATTTTATTTT
1 ATTTTAATTTCTTAT-TTTTATATT
*
5984783 ATTTTAATTTTTTATTTTTATATT
1 ATTTTAATTTCTTATTTTTATATT
5984807 AT
1 AT
5984809 ATATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
ATTTTAATTTCTTATTTTTATATT
Found at i:5984806 original size:55 final size:57
Alignment explanation
Indices: 5984705--5984912 Score: 145
Period size: 55 Copynumber: 3.6 Consensus size: 57
5984695 TTTTTTAATA
* *
5984705 TAATTTTTTATATTATATATTTTATTTTTATTTCTTTTACCTATATTATATAAATTT
1 TAATTTCTTATATTATATATTTTATTTTAATTTCTTTTACCTATATTATATAAATTT
*** *
5984762 TAATTTCTTATATT-T-TATTTTATTTTAATTT-TTTATTTTTATATTATATATTTTATTT
1 TAATTTCTTATATTATATATTTTATTTTAATTTCTTT-TACCTATATTATATA---AATTT
* * ** * ** * * *
5984820 TAATTTCTTTTACCTATATTATATAAATTTTAATTTCTTATATTTTATTTTATTTTAATTTT
1 TAATTTCTTATA-TTATA-TAT-TTTATTTTAATTTCTTTTA-CCTATATTA-TATAAATTT
* *
5984882 TGATTT-TTATATTATATGTTTTATTTTAATT
1 TAATTTCTTATATTATATATTTTATTTTAATT
5984913 ATAATGCTAC
Statistics
Matches: 117, Mismatches: 22, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
54 3 0.03
55 27 0.23
56 1 0.01
57 13 0.11
58 25 0.21
59 3 0.03
60 5 0.04
61 4 0.03
62 11 0.09
63 12 0.10
64 10 0.09
65 3 0.03
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (57 bp):
TAATTTCTTATATTATATATTTTATTTTAATTTCTTTTACCTATATTATATAAATTT
Found at i:5984838 original size:33 final size:33
Alignment explanation
Indices: 5984770--5984844 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
5984760 TTTAATTTCT
***
5984770 TATATT-T-TATTTTATTTTAATTTTTTATTTT
1 TATATTATATATTTTATTTTAATTTTTTATACC
5984801 TATATTATATATTTTATTTTAATTTCTTT-TACC
1 TATATTATATATTTTATTTTAATTT-TTTATACC
5984834 TATATTATATA
1 TATATTATATA
5984845 AATTTTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.16
32 1 0.03
33 28 0.74
34 3 0.08
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (33 bp):
TATATTATATATTTTATTTTAATTTTTTATACC
Found at i:5998357 original size:29 final size:29
Alignment explanation
Indices: 5998316--5998392 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
5998306 TTCACTCAAA
* *
5998316 AATAAAA-TATAAAAATTTAATTGTATGT
1 AATAAAAGAATAAAAATTTAATTATATGT
5998344 AATAAAAGAATAAAAATTTAATTATATGT
1 AATAAAAGAATAAAAATTTAATTATATGT
5998373 AATAAAAGAATAAAAATTTA
1 AATAAAAGAATAAAAATTTA
5998393 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (29 bp):
AATAAAAGAATAAAAATTTAATTATATGT
Found at i:5999194 original size:26 final size:27
Alignment explanation
Indices: 5999165--5999215 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5999155 ATAAAAAATT
*
5999165 TAAATT-TATAAAATTAATATTTTAAA
1 TAAATTATAAAAAATTAATATTTTAAA
5999191 TAAATTATAAAAAATTAATATTTTA
1 TAAATTATAAAAAATTAATATTTTA
5999216 TATTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAATTATAAAAAATTAATATTTTAAA
Found at i:5999430 original size:51 final size:51
Alignment explanation
Indices: 5999369--5999471 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
5999359 ATTATATATT
*
5999369 ATAAAATATTTTGAATTTAAAAATT-AATTA-AAAGTATTAATATTTT-AATC
1 ATAAAATA-TTT-AAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
* * *
5999419 ATAATAATATTTAAATTATAAATTAAATTACCAATTATTAATATTTTCAATC
1 ATAA-AATATTTAAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
5999471 A
1 A
5999472 ATTATAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 10 0.22
50 12 0.27
51 18 0.40
52 5 0.11
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (51 bp):
ATAAAATATTTAAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
Found at i:5999439 original size:17 final size:17
Alignment explanation
Indices: 5999406--5999439 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5999396 TTAAAAGTAT
*
5999406 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
5999423 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
5999440 ATTAAATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Done.