Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 68 of 318
Found at i:23995540 original size:29 final size:27
Alignment explanation
Indices: 23995485--23995541 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
23995475 ATTTTTATAT
* *
23995485 ATAGTTTTAAAAAATATTCAGTGTTTA
1 ATAGTTTTAAAAAACATTCAGTATTTA
*
23995512 ATAGTGTTTAAAAAACATTCATTAATTTA
1 ATAGT-TTTAAAAAACATTCAGT-ATTTA
23995541 A
1 A
23995542 CTTTCATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.20
28 15 0.60
29 5 0.20
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (27 bp):
ATAGTTTTAAAAAACATTCAGTATTTA
Found at i:24001781 original size:16 final size:17
Alignment explanation
Indices: 24001760--24001793 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24001750 ATTAAAAGAA
24001760 AAGGAAAGATT-TTTAC
1 AAGGAAAGATTGTTTAC
*
24001776 AAGGAAAGGTTGTTTAC
1 AAGGAAAGATTGTTTAC
24001793 A
1 A
24001794 GAGAGAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
AAGGAAAGATTGTTTAC
Found at i:24006250 original size:31 final size:31
Alignment explanation
Indices: 24006181--24006260 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
24006171 TTGCTTTATG
* * * *
24006181 TAGTACTATTTGCTTTATGTAATAATGTCTA
1 TAGTACTGTTTGCTTTAGGAAATAATGACTA
24006212 TAGTACTGTTTGCTTTAGGAAATAATGACTA
1 TAGTACTGTTTGCTTTAGGAAATAATGACTA
* *
24006243 TAGTACTGTCTACTTTAG
1 TAGTACTGTTTGCTTTAG
24006261 TACTATTTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (31 bp):
TAGTACTGTTTGCTTTAGGAAATAATGACTA
Found at i:24008906 original size:40 final size:40
Alignment explanation
Indices: 24008856--24008939 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
24008846 AATTATGGAA
* * * *
24008856 TACTGAATATTGTTTTG-AGTACTGGATTGAATTGTGAAGT
1 TACTGAATATTGTTATGTA-TACTGCATTGAACTGTGAAAT
24008896 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
24008936 TACT
1 TACT
24008940 AAAGTAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (40 bp):
TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
Found at i:24009212 original size:44 final size:45
Alignment explanation
Indices: 24009133--24009245 Score: 149
Period size: 44 Copynumber: 2.5 Consensus size: 45
24009123 CAGGCACTTA
* * * *
24009133 TGTGCCGACTACTGTTACTGTTACTGTTACGGATTC-GACACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGTTACCGATTCAG-CACTTTG
24009178 TGTGTCGAATACTGTTACTG-TACCGTTACCGATTCAGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGTTACCGATTCAGCACTTTG
* *
24009222 TGTGTTGAATACTGTTACTATTAC
1 TGTGTCGAATACTGTTACTGTTAC
24009246 TGCTACTGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
44 38 0.63
45 22 0.37
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (45 bp):
TGTGTCGAATACTGTTACTGTTACCGTTACCGATTCAGCACTTTG
Found at i:24010506 original size:61 final size:59
Alignment explanation
Indices: 24010399--24010552 Score: 229
Period size: 61 Copynumber: 2.6 Consensus size: 59
24010389 ACAAAGTTGA
** * *
24010399 ATAGTTGGGTGACCAAAAAAGAAATTTACTAATACTTGGGTAACCATTTTGTAACTTTTT
1 ATAGTTGGGTGACCAAAAAA-AAATTTACTAATAGATGAGTAACCATTTTGTAACTTTTC
*
24010459 ATAGTTGGGTGACCAAAAAATTAAATTTACTAATAGATGAGTGACCATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAA--AAATTTACTAATAGATGAGTAACCATTTTGTAACTTTTC
24010520 ATAGTTGGGTGACC-AAAAAAAATTTACTAATAG
1 ATAGTTGGGTGACCAAAAAAAAATTTACTAATAG
24010553 TTGAATGTCT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
58 14 0.16
60 25 0.29
61 48 0.55
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (59 bp):
ATAGTTGGGTGACCAAAAAAAAATTTACTAATAGATGAGTAACCATTTTGTAACTTTTC
Found at i:24010531 original size:29 final size:29
Alignment explanation
Indices: 24010428--24010534 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 29
24010418 AGAAATTTAC
* *
24010428 TAATACTTGGGTAACCATTTTGTAACTTT
1 TAATAGTTGGGTGACCATTTTGTAACTTT
* *** *
24010457 TTATAGTTGGGTGACCAAAAAAT-TAAATTT
1 TAATAGTTGGGTGACC--ATTTTGTAACTTT
* *
24010487 ACTAATAGATGAGTGACCATTTTGTAACTTT
1 --TAATAGTTGGGTGACCATTTTGTAACTTT
*
24010518 TCATAGTTGGGTGACCA
1 TAATAGTTGGGTGACCA
24010535 AAAAAAATTT
Statistics
Matches: 56, Mismatches: 17, Indels: 10
0.67 0.20 0.12
Matches are distributed among these distances:
29 27 0.48
30 8 0.14
31 8 0.14
32 13 0.23
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (29 bp):
TAATAGTTGGGTGACCATTTTGTAACTTT
Found at i:24011830 original size:21 final size:20
Alignment explanation
Indices: 24011802--24011847 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
24011792 TGTGGTGAAA
* *
24011802 ATTAATAAATTTTAATATAT
1 ATTAATAAATATAAATATAT
24011822 ATTATATAAATATAAATATAT
1 ATTA-ATAAATATAAATATAT
24011843 ATTAA
1 ATTAA
24011848 AATAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAATAAATATAAATATAT
Found at i:24011860 original size:21 final size:20
Alignment explanation
Indices: 24011814--24011861 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
24011804 TAATAAATTT
*
24011814 TAATATATATTATATAAATA
1 TAATATATATTAAATAAATA
24011834 TAAATATATATTAAA-ATAATAA
1 T-AATATATATTAAATA-AAT-A
24011856 TAATAT
1 TAATAT
24011862 TAGATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATATATATTAAATAAATA
Found at i:24016602 original size:20 final size:21
Alignment explanation
Indices: 24016572--24016619 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
24016562 CGTTAATCAT
24016572 ATTAA-TTTTTAATAATAAA-A
1 ATTAATTTTTTAATAA-AAATA
24016592 A-TAATTTTTTAATAAAAATA
1 ATTAATTTTTTAATAAAAATA
24016612 ATTAATTT
1 ATTAATTT
24016620 ATTATTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 13 0.52
21 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATTTTTTAATAAAAATA
Found at i:24016606 original size:17 final size:18
Alignment explanation
Indices: 24016574--24016614 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
24016564 TTAATCATAT
24016574 TAATTTTTAATAATAAAAA
1 TAATTTTT-ATAATAAAAA
24016593 TAATTTTT-TAATAAAAA
1 TAATTTTTATAATAAAAA
24016610 TAATT
1 TAATT
24016615 AATTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.64
19 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTTTTATAATAAAAA
Found at i:24023866 original size:3 final size:3
Alignment explanation
Indices: 24023854--24023895 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
24023844 ATATACACGA
24023854 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
24023896 TTAGCTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:24025733 original size:31 final size:31
Alignment explanation
Indices: 24025697--24025760 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
24025687 CTAGCGAGGG
* *
24025697 ACCTACCACCTACGATCTAGGAGCCTCACAT
1 ACCTACCACCTACGATCCAAGAGCCTCACAT
24025728 ACCTACCACCTACGATCCAAGAGCCTCACAT
1 ACCTACCACCTACGATCCAAGAGCCTCACAT
24025759 AC
1 AC
24025761 TCAGTGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.41, G:0.11, T:0.17
Consensus pattern (31 bp):
ACCTACCACCTACGATCCAAGAGCCTCACAT
Found at i:24029419 original size:21 final size:21
Alignment explanation
Indices: 24029393--24029433 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24029383 AAGAAATATA
*
24029393 TAAATTAATTAATACTTTTTT
1 TAAATTAATTAATAATTTTTT
**
24029414 TAAATTTTTTAATAATTTTT
1 TAAATTAATTAATAATTTTT
24029434 AATAAACTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TAAATTAATTAATAATTTTTT
Found at i:24033660 original size:12 final size:12
Alignment explanation
Indices: 24033643--24033667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24033633 TTGGGTATTG
24033643 TGTGTATATATA
1 TGTGTATATATA
24033655 TGTGTATATATA
1 TGTGTATATATA
24033667 T
1 T
24033668 ATGACTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TGTGTATATATA
Found at i:24033664 original size:14 final size:14
Alignment explanation
Indices: 24033641--24033670 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24033631 GGTTGGGTAT
*
24033641 TGTGTGTATATATA
1 TGTGTATATATATA
24033655 TGTGTATATATATA
1 TGTGTATATATATA
24033669 TG
1 TG
24033671 ACTATTTCAT
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:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (14 bp):
TGTGTATATATATA
Found at i:24047452 original size:22 final size:20
Alignment explanation
Indices: 24047412--24047475 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
24047402 TTCAGATGTC
*
24047412 TTTAGTTATTTTATATCATA
1 TTTAATTATTTTATATCATA
24047432 TTTAATTATTTTTCATATCATA
1 TTTAATTA-TTTT-ATATCATA
*
24047454 TTATAA--ATTTTATGTCATA
1 TT-TAATTATTTTATATCATA
24047473 TTT
1 TTT
24047476 GATGCCATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 1 0.03
19 9 0.23
20 11 0.28
21 5 0.13
22 10 0.26
23 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTAATTATTTTATATCATA
Found at i:24052283 original size:38 final size:39
Alignment explanation
Indices: 24052199--24052292 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 39
24052189 ACCAATATGG
24052199 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
* * *
24052238 CACCCAGTGTCTCATCGGCCTAG-TCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTTCGAAGTAATAGTTGA
* *
24052276 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
24052293 AATCTATCCG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 19 0.40
39 26 0.54
40 3 0.06
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
Found at i:24053911 original size:5 final size:5
Alignment explanation
Indices: 24053893--24053923 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
24053883 TTTCTTTTAT
24053893 ATATA ATAATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA
24053924 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:24054889 original size:13 final size:13
Alignment explanation
Indices: 24054873--24054897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24054863 AATATTTTAG
24054873 AAATAAAAAATAA
1 AAATAAAAAATAA
24054886 AAATAAAAAATA
1 AAATAAAAAATA
24054898 TGTAATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:24072959 original size:19 final size:19
Alignment explanation
Indices: 24072909--24072961 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
24072899 ATGAAATATT
* *
24072909 TATTTAATTTAATTTTTAC
1 TATTTAATTTAATTTTAAA
*
24072928 TACTTAATGTTAATTTTAAA
1 TATTTAAT-TTAATTTTAAA
*
24072948 TATTTTATTTAATT
1 TATTTAATTTAATT
24072962 AAAAATGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTAATTTAATTTTAAA
Found at i:24082728 original size:6 final size:6
Alignment explanation
Indices: 24082717--24082742 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
24082707 GACGAGTAAT
24082717 TCTGTC TCTGTC TCTGTC TCTGTC TC
1 TCTGTC TCTGTC TCTGTC TCTGTC TC
24082743 CACCGATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.15, T:0.50
Consensus pattern (6 bp):
TCTGTC
Found at i:24085702 original size:21 final size:21
Alignment explanation
Indices: 24085654--24085703 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
24085644 ATTGAATCAA
24085654 AATAAATAACAAAAAAAAATT
1 AATAAATAACAAAAAAAAATT
* *
24085675 AAAAAATACCAAAATAAAAA-T
1 AATAAATAACAAAA-AAAAATT
*
24085696 ATTAAATA
1 AATAAATA
24085704 TATTTCAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (21 bp):
AATAAATAACAAAAAAAAATT
Found at i:24087159 original size:19 final size:19
Alignment explanation
Indices: 24087120--24087159 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24087110 ATTACTTTTT
*
24087120 AAAAATACTTTTGAAATAA
1 AAAAATACTTTTGAAACAA
* *
24087139 AAAAATATTTTTGAGACAA
1 AAAAATACTTTTGAAACAA
24087158 AA
1 AA
24087160 GCATTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAAATACTTTTGAAACAA
Found at i:24094688 original size:16 final size:16
Alignment explanation
Indices: 24094667--24094729 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
24094657 ACTTTTCTAA
24094667 AAATAAATTACTAATT
1 AAATAAATTACTAATT
*
24094683 AAATAAATTAATAATTT
1 AAATAAATTACTAA-TT
*
24094700 AAACT--ATT-TTAATT
1 AAA-TAAATTACTAATT
24094714 AAATAAATTACTAATT
1 AAATAAATTACTAATT
24094730 TTTTATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 1 0.03
14 5 0.13
15 6 0.15
16 21 0.54
17 5 0.13
18 1 0.03
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAAATTACTAATT
Found at i:24094978 original size:37 final size:36
Alignment explanation
Indices: 24094915--24094985 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
24094905 TCAAGGATCA
*
24094915 AATTTTAATAAATAAAAATAAATAAATTGACTTCTT
1 AATTTTAATAAATAAAAATAAATAAATTCACTTCTT
* *
24094951 AATTTTTATAAAATAAAAA-AATTTAAATTCACTTC
1 AATTTTAAT-AAATAAAAATAA-ATAAATTCACTTC
24094986 AAGCGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 10 0.33
37 20 0.67
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (36 bp):
AATTTTAATAAATAAAAATAAATAAATTCACTTCTT
Found at i:24104115 original size:27 final size:27
Alignment explanation
Indices: 24104073--24104128 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
24104063 GGTTCAATAA
24104073 ATAATTTTTTTCAATAATAGAATTTTC
1 ATAATTTTTTTCAATAATAGAATTTTC
* *
24104100 ATAATTTTTTTGAATAATATAATTTTC
1 ATAATTTTTTTCAATAATAGAATTTTC
24104127 AT
1 AT
24104129 TCATTTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (27 bp):
ATAATTTTTTTCAATAATAGAATTTTC
Found at i:24107811 original size:30 final size:30
Alignment explanation
Indices: 24107777--24107838 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
24107767 CAACTTAACA
*
24107777 AACAAATGT-TTCTTAAATAATAATAAAATT
1 AACAAATGTCTT-TAAAATAATAATAAAATT
24107807 AACAAATGTCTTTAAAATAATAATAAAATT
1 AACAAATGTCTTTAAAATAATAATAAAATT
24107837 AA
1 AA
24107839 TAAAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (30 bp):
AACAAATGTCTTTAAAATAATAATAAAATT
Found at i:24107896 original size:22 final size:22
Alignment explanation
Indices: 24107871--24107913 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24107861 TATCCAAACA
24107871 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
24107893 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
24107914 AATGAGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:24108417 original size:12 final size:12
Alignment explanation
Indices: 24108400--24108458 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
24108390 AAGATTGTAA
24108400 TATTAAATATAT
1 TATTAAATATAT
24108412 TATTAAATA-ATT
1 TATTAAATATA-T
*
24108424 TATTATAT-TAAT
1 TATTAAATAT-AT
*
24108436 AATTAAATATAT
1 TATTAAATATAT
24108448 TATTAAATATA
1 TATTAAATATA
24108459 AATAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 1 0.03
12 36 0.92
13 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATTAAATATAT
Found at i:24108427 original size:24 final size:24
Alignment explanation
Indices: 24108400--24108471 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
24108390 AAGATTGTAA
*
24108400 TATTAAATATATTATTAAATA-ATT
1 TATTAAATATATAATTAAATATA-T
*
24108424 TATTATAT-TAATAATTAAATATAT
1 TATTAAATAT-ATAATTAAATATAT
24108448 TATTAAATATAAATAATTAAATAT
1 TATTAAATAT--ATAATTAAATAT
24108472 TATGTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 25 0.61
25 2 0.05
26 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTAAATATATAATTAAATATAT
Found at i:24108438 original size:16 final size:16
Alignment explanation
Indices: 24108412--24108467 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
24108402 TTAAATATAT
* *
24108412 TATTAAATAATTTATTA
1 TATT-AATAATTAAATA
24108429 TATTAATAATTAAATA
1 TATTAATAATTAAATA
*
24108445 TATTATTAAATATAAATA
1 TATTAAT-AAT-TAAATA
24108463 -ATTAA
1 TATTAA
24108468 ATATTATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 16 0.48
17 11 0.33
18 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATAATTAAATA
Found at i:24108468 original size:14 final size:13
Alignment explanation
Indices: 24108397--24108471 Score: 61
Period size: 12 Copynumber: 6.1 Consensus size: 13
24108387 AATAAGATTG
24108397 TAAT-ATTAAATA
1 TAATAATTAAATA
*
24108409 T-ATTATTAAATA
1 TAATAATTAAATA
* * *
24108421 -ATTTATTATAT-
1 TAATAATTAAATA
24108432 TAATAATTAAATA
1 TAATAATTAAATA
*
24108445 T-ATTATTAAATA
1 TAATAATTAAATA
24108457 TAAATAATTAAATA
1 T-AATAATTAAATA
24108471 T
1 T
24108472 TATGTTTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.04
12 36 0.72
13 1 0.02
14 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATAATTAAATA
Found at i:24112001 original size:4 final size:4
Alignment explanation
Indices: 24111992--24112023 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
24111982 CAAAAAAGGC
24111992 TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA
24112024 GATTGGTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:24115039 original size:26 final size:26
Alignment explanation
Indices: 24115003--24115066 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
24114993 CAAGATTAAA
*
24115003 AAACACTTTAAATAA-AAAATAATTTT-
1 AAACAATTTAAA-AATAAAAT-ATTTTC
24115029 AAACAATTTAAAAATAAAATATTTTC
1 AAACAATTTAAAAATAAAATATTTTC
*
24115055 AAA-AATTCAAAA
1 AAACAATTTAAAA
24115067 CATGTGTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (26 bp):
AAACAATTTAAAAATAAAATATTTTC
Found at i:24116024 original size:9 final size:8
Alignment explanation
Indices: 24115977--24116024 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 8
24115967 TCGTTTATAT
24115977 TTTTAATAA
1 TTTTAA-AA
*
24115986 TTTTAGAA
1 TTTTAAAA
24115994 TTTTATAAA
1 TTTTA-AAA
24116003 TTTTAAAA
1 TTTTAAAA
24116011 TTTTTAAAGA
1 -TTTTAAA-A
24116021 TTTT
1 TTTT
24116025 TTTTTGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 10 0.29
9 23 0.68
10 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:24119955 original size:13 final size:13
Alignment explanation
Indices: 24119916--24119966 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
24119906 AGTTCTTCAT
24119916 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
24119929 TACTGTAGAAAAG
1 TGCTTTTGAAAAG
*
24119942 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
24119955 TGCTTTAGAAAA
1 TGCTTTTGAAAA
24119967 ATTTAAGTGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:24119955 original size:26 final size:26
Alignment explanation
Indices: 24119916--24119966 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
24119906 AGTTCTTCAT
24119916 TGCTTTTGAAAAGTACTGTAGAAAAG
1 TGCTTTTGAAAAGTACTGTAGAAAAG
* * *
24119942 TGCTTTTGAGAAGTGCTTTAGAAAA
1 TGCTTTTGAAAAGTACTGTAGAAAA
24119967 ATTTAAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTGTAGAAAAG
Found at i:24141758 original size:5 final size:5
Alignment explanation
Indices: 24141748--24141772 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
24141738 ACATAGAAAT
24141748 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
24141773 GATTAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:24153163 original size:26 final size:27
Alignment explanation
Indices: 24153125--24153177 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
24153115 ACTTCATGTC
24153125 AACAAATAA-TT-TAAAAATTATAAAAA
1 AACAAATAATTTATAAAAATT-TAAAAA
24153151 AACAAA-AATTTTATAAAAATTTAAAAA
1 AACAAATAA-TTTATAAAAATTTAAAAA
24153178 TAAAATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 2 0.08
26 6 0.25
27 8 0.33
28 8 0.33
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (27 bp):
AACAAATAATTTATAAAAATTTAAAAA
Found at i:24153176 original size:19 final size:18
Alignment explanation
Indices: 24153132--24153178 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
24153122 GTCAACAAAT
24153132 AATTTAAAAA-TTATAAA
1 AATTTAAAAATTTATAAA
***
24153149 AAAACAAAAATTTTATAAA
1 AATTTAAAAA-TTTATAAA
24153168 AATTTAAAAAT
1 AATTTAAAAAT
24153179 AAAATTAACA
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTTAAAAATTTATAAA
Found at i:24156249 original size:29 final size:31
Alignment explanation
Indices: 24156191--24156252 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
24156181 ATTTTAAAAT
* * *
24156191 TATATATGAATTTTAGTTTAATGTATAATTG
1 TATATATAAATTTTAATTTAATGTACAATTG
24156222 TATATATAAATTTTAATTT-A-GTACAATTG
1 TATATATAAATTTTAATTTAATGTACAATTG
24156251 TA
1 TA
24156253 CACTTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
30 1 0.04
31 17 0.61
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.50
Consensus pattern (31 bp):
TATATATAAATTTTAATTTAATGTACAATTG
Found at i:24157518 original size:18 final size:19
Alignment explanation
Indices: 24157495--24157534 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
24157485 AGTCTATGTA
24157495 TAAAA-TTATACATTAAAT
1 TAAAATTTATACATTAAAT
* *
24157513 TAAAATTTATCCCTTAAAT
1 TAAAATTTATACATTAAAT
24157532 TAA
1 TAA
24157535 TGATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATTTATACATTAAAT
Found at i:24164682 original size:30 final size:31
Alignment explanation
Indices: 24164627--24164687 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
24164617 AATAAGCAAA
24164627 TGCCTCTAAAATAATAACAAAAATTAACAAT
1 TGCCTCTAAAATAATAACAAAAATTAACAAT
*
24164658 TGCCTTTAAAATAATAAC-AAAATTAACAAT
1 TGCCTCTAAAATAATAACAAAAATTAACAAT
24164688 AAAATAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (31 bp):
TGCCTCTAAAATAATAACAAAAATTAACAAT
Found at i:24168169 original size:3 final size:3
Alignment explanation
Indices: 24168107--24168149 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
24168097 TTGGGCTTCA
* * *
24168107 CTT CTT CTT CTT CTT CTT CTT CCT CTT CGT CTT CTT CTC CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
24168150 ATCATCACCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (3 bp):
CTT
Found at i:24172641 original size:29 final size:29
Alignment explanation
Indices: 24172602--24172675 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 29
24172592 GTGGAAAATG
24172602 TTTTTTAGAAAAAGAGTTCCTTTATAACA
1 TTTTTTAGAAAAAGAGTTCCTTTATAACA
*
24172631 TTTTTTGGAAAAAGAGTTCCTTTATAACA
1 TTTTTTAGAAAAAGAGTTCCTTTATAACA
24172660 TGATTTTTAGATAAAA
1 T--TTTTTAGA-AAAA
24172676 CTTATGTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 29 0.73
31 7 0.17
32 4 0.10
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (29 bp):
TTTTTTAGAAAAAGAGTTCCTTTATAACA
Found at i:24187242 original size:21 final size:21
Alignment explanation
Indices: 24187208--24187251 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
24187198 AATTATTAAA
*
24187208 ATATTCTTATTTGTATTAATT
1 ATATTCTTACTTGTATTAATT
*
24187229 ATATTTTTACTTGTATTAATT
1 ATATTCTTACTTGTATTAATT
24187250 AT
1 AT
24187252 TTAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
ATATTCTTACTTGTATTAATT
Found at i:24187376 original size:34 final size:34
Alignment explanation
Indices: 24187296--24187386 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 34
24187286 TTCTATTTAA
* * *
24187296 ATATTAAACTATTT-AAATA--TTATTTATTATT
1 ATATTAAAATATTTAAAATATTTTATGTATAATT
24187327 ATATTTAAAAT-TTTAAAATATTTTATGTATAATT
1 ATA-TTAAAATATTTAAAATATTTTATGTATAATT
* *
24187361 ATATTAAATTATTTAAATTATTTTAT
1 ATATTAAAATATTTAAAATATTTTAT
24187387 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
31 6 0.12
32 11 0.22
33 6 0.12
34 27 0.54
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
ATATTAAAATATTTAAAATATTTTATGTATAATT
Found at i:24188728 original size:19 final size:20
Alignment explanation
Indices: 24188706--24188752 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
24188696 AAAAAATTTA
24188706 TATTATTTTAATTTA-ATAT
1 TATTATTTTAATTTAGATAT
*
24188725 TATTA-TTTATTTTAGATAT
1 TATTATTTTAATTTAGATAT
24188744 T-TTATTTTA
1 TATTATTTTA
24188753 GTAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTATTTTAATTTAGATAT
Found at i:24188761 original size:42 final size:43
Alignment explanation
Indices: 24188678--24188763 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 43
24188668 AAACTCGTAC
* **
24188678 ATATTATTATTTTATTTTAAAAAATTTATATTATTTTAATTTA
1 ATATTATTATTTTATTTTAAAAAATTTATATTAGTAAAATTTA
* * * *
24188721 ATATTATTA-TTTATTTTAGATATTTTATTTTAGTAAAATTTA
1 ATATTATTATTTTATTTTAAAAAATTTATATTAGTAAAATTTA
24188763 A
1 A
24188764 AACATAAGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 27 0.75
43 9 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (43 bp):
ATATTATTATTTTATTTTAAAAAATTTATATTAGTAAAATTTA
Found at i:24188852 original size:21 final size:18
Alignment explanation
Indices: 24188828--24188867 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 18
24188818 TATTTGATAT
24188828 AAATTACATAATATATAAAAA
1 AAATTACA-AA-ATA-AAAAA
24188849 AAATTACAAAATAAAAAA
1 AAATTACAAAATAAAAAA
24188867 A
1 A
24188868 GCCATGCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 2 0.11
21 8 0.42
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATTACAAAATAAAAAA
Found at i:24193007 original size:57 final size:57
Alignment explanation
Indices: 24192919--24193046 Score: 229
Period size: 57 Copynumber: 2.2 Consensus size: 57
24192909 TTAACATGAG
24192919 CCTAAAGTCACCAAAATAGAAACAGGGCCTACCTAAATTGATTCTAAAGGACCCAAA
1 CCTAAAGTCACCAAAATAGAAACAGGGCCTACCTAAATTGATTCTAAAGGACCCAAA
* * *
24192976 CCTAAAGTTACCAAAATGGAAACAGGTCCTACCTAAATTGATTCTAAAGGACCCAAA
1 CCTAAAGTCACCAAAATAGAAACAGGGCCTACCTAAATTGATTCTAAAGGACCCAAA
24193033 CCTAAAGTCACCAA
1 CCTAAAGTCACCAA
24193047 GAAACCCAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 67 1.00
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.19
Consensus pattern (57 bp):
CCTAAAGTCACCAAAATAGAAACAGGGCCTACCTAAATTGATTCTAAAGGACCCAAA
Found at i:24196141 original size:26 final size:26
Alignment explanation
Indices: 24196088--24196162 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
24196078 CTATATTTTC
*
24196088 AAATTAAACGATGA-TTAAATTAATA
1 AAATTAAACCATGATTTAAATTAATA
*
24196113 AAATTAAACCATGATTTGAATTAATA
1 AAATTAAACCATGATTTAAATTAATA
*
24196139 AAACTAAACCATGATTTAAATTAA
1 AAATTAAACCATGATTTAAATTAA
24196163 CACTTTGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 13 0.29
26 32 0.71
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (26 bp):
AAATTAAACCATGATTTAAATTAATA
Found at i:24205168 original size:3 final size:3
Alignment explanation
Indices: 24205160--24205184 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24205150 AAAAGAAAGT
24205160 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
24205185 AGGAACACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:24206145 original size:2 final size:2
Alignment explanation
Indices: 24206134--24206164 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24206124 TCAAAGCAAC
24206134 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
24206165 TTTTGGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:24213418 original size:24 final size:24
Alignment explanation
Indices: 24213391--24213442 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
24213381 TTAGTAAGTC
*
24213391 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
24213415 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
24213439 AAAT
1 AAAT
24213443 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:24215387 original size:24 final size:24
Alignment explanation
Indices: 24215360--24215411 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
24215350 TTAGTAAGTC
*
24215360 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
24215384 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
24215408 AAAT
1 AAAT
24215412 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:24216007 original size:3 final size:3
Alignment explanation
Indices: 24215997--24216027 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
24215987 TTGTAACAAC
24215997 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
24216028 CCAAACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:24228749 original size:22 final size:22
Alignment explanation
Indices: 24228721--24228764 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24228711 ACATTAAGAG
24228721 TAAAAAAACATACTAATACATT
1 TAAAAAAACATACTAATACATT
*
24228743 TAAAAAAACATATTAATACATT
1 TAAAAAAACATACTAATACATT
24228765 ATATACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAAAACATACTAATACATT
Found at i:24229542 original size:409 final size:409
Alignment explanation
Indices: 24228783--24229600 Score: 1627
Period size: 409 Copynumber: 2.0 Consensus size: 409
24228773 AATTAATTTT
24228783 ATTTATTAACAAGCATATAACCCCATTTACTCATTACTTGCCTTTATTCTTATTAATTTGTGCTA
1 ATTTATTAACAAGCATATAACCCCATTTACTCATTACTTGCCTTTATTCTTATTAATTTGTGCTA
*
24228848 TGCATTTGAATCAACCCGTTTTAGATTGTGATAAATGTGATCAATTAGAACAAACAATCCACTCT
66 TGCATTTGAATCAACCCGTTTTAGATTATGATAAATGTGATCAATTAGAACAAACAATCCACTCT
24228913 TTAAGCATTATGGAACTCAAGTCATTGGAGATTCGCCTTTGAAATCGTTTACGTTTTATTCTCAG
131 TTAAGCATTATGGAACTCAAGTCATTGGAGATTCGCCTTTGAAATCGTTTACGTTTTATTCTCAG
24228978 ATTAATTTTGGTTTAAAGCCCAGTTAAGAAACTTCCGTTGATGAGACATGAAGAGAAGCGAGGGA
196 ATTAATTTTGGTTTAAAGCCCAGTTAAGAAACTTCCGTTGATGAGACATGAAGAGAAGCGAGGGA
24229043 AAGGGAGAAAAAAATGAAGGTGTCAAACTTTTACAAGTTGCTTAGAAAATCTGAAAAACAAAAAA
261 AAGGGAGAAAAAAATGAAGGTGTCAAACTTTTACAAGTTGCTTAGAAAATCTGAAAAACAAAAAA
24229108 CAACAGCTGGGATCTACTCTTCTTCTTCATCGGTGAGAAATTTACCAGTCCCAGGGTTTATAGCA
326 CAACAGCTGGGATCTACTCTTCTTCTTCATCGGTGAGAAATTTACCAGTCCCAGGGTTTATAGCA
24229173 GCAAAGAAGAAGAAAGCAA
391 GCAAAGAAGAAGAAAGCAA
24229192 ATTTATTAACAAGCATATAACCCCATTTACTCATTACTTGCCTTTATTCTTATTAATTTGTGCTA
1 ATTTATTAACAAGCATATAACCCCATTTACTCATTACTTGCCTTTATTCTTATTAATTTGTGCTA
24229257 TGCATTTGAATCAACCCGTTTTAGATTATGATAAATGTGATCAATTAGAACAAACAATCCACTCT
66 TGCATTTGAATCAACCCGTTTTAGATTATGATAAATGTGATCAATTAGAACAAACAATCCACTCT
24229322 TTAAGCATTATGGAACTCAAGTCATTGGAGATTCGCCTTTGAAATCGTTTACGTTTTATTCTCAG
131 TTAAGCATTATGGAACTCAAGTCATTGGAGATTCGCCTTTGAAATCGTTTACGTTTTATTCTCAG
24229387 ATTAATTTTGGTTTAAAGCCCAGTTAAGAAACTTCCGTTGATGAGACATGAAGAGAAGCGAGGGA
196 ATTAATTTTGGTTTAAAGCCCAGTTAAGAAACTTCCGTTGATGAGACATGAAGAGAAGCGAGGGA
24229452 AAGGGAGAAAAAAATGAAGGTGTCAAACTTTTACAAGTTGCTTAGAAAATCTGAAAAACAAAAAA
261 AAGGGAGAAAAAAATGAAGGTGTCAAACTTTTACAAGTTGCTTAGAAAATCTGAAAAACAAAAAA
24229517 CAACAGCTGGGATCTACTCTTCTTCTTCATCGGTGAGAAATTTACCAGTCCCAGGGTTTATAGCA
326 CAACAGCTGGGATCTACTCTTCTTCTTCATCGGTGAGAAATTTACCAGTCCCAGGGTTTATAGCA
24229582 GCAAAGAAGAAGAAAGCAA
391 GCAAAGAAGAAGAAAGCAA
24229601 CGTTGAACAA
Statistics
Matches: 408, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
409 408 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (409 bp):
ATTTATTAACAAGCATATAACCCCATTTACTCATTACTTGCCTTTATTCTTATTAATTTGTGCTA
TGCATTTGAATCAACCCGTTTTAGATTATGATAAATGTGATCAATTAGAACAAACAATCCACTCT
TTAAGCATTATGGAACTCAAGTCATTGGAGATTCGCCTTTGAAATCGTTTACGTTTTATTCTCAG
ATTAATTTTGGTTTAAAGCCCAGTTAAGAAACTTCCGTTGATGAGACATGAAGAGAAGCGAGGGA
AAGGGAGAAAAAAATGAAGGTGTCAAACTTTTACAAGTTGCTTAGAAAATCTGAAAAACAAAAAA
CAACAGCTGGGATCTACTCTTCTTCTTCATCGGTGAGAAATTTACCAGTCCCAGGGTTTATAGCA
GCAAAGAAGAAGAAAGCAA
Found at i:24233268 original size:19 final size:19
Alignment explanation
Indices: 24233244--24233280 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24233234 GTTAATATAA
24233244 ATTAATAAA-ATTACTTTTT
1 ATTAATAAATATTA-TTTTT
24233263 ATTAATAAATATTATTTT
1 ATTAATAAATATTATTTT
24233281 AGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTAATAAATATTATTTTT
Found at i:24235414 original size:39 final size:41
Alignment explanation
Indices: 24235369--24235446 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
24235359 AAAATGATTA
* *
24235369 AAAATTAAAAAA-ATTATAAAAA-ATAAAATATTTAATATT
1 AAAATTAAAAAATATTATAAAAATATAAAAAATCTAATATT
*
24235408 AAAATTAAAAAATGTTATAAAAATATAAAAAATCTAATA
1 AAAATTAAAAAATATTATAAAAATATAAAAAATCTAATA
24235447 AATTATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 12 0.35
40 9 0.26
41 13 0.38
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (41 bp):
AAAATTAAAAAATATTATAAAAATATAAAAAATCTAATATT
Found at i:24235474 original size:19 final size:18
Alignment explanation
Indices: 24235407--24235470 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
24235397 TATTTAATAT
*
24235407 TAAAATTAAAAAATGTTA
1 TAAAATTAAAAAATCTTA
*
24235425 TAAAAATATAAAAAATCTAA
1 T-AAAAT-TAAAAAATCTTA
* *
24235445 T-AAATTATAAAATTTTA
1 TAAAATTAAAAAATCTTA
24235462 TAAAATTAA
1 TAAAATTAA
24235471 TAAACATACT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 10 0.27
18 11 0.30
19 5 0.14
20 11 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAAATTAAAAAATCTTA
Found at i:24236024 original size:20 final size:19
Alignment explanation
Indices: 24235999--24236046 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
24235989 TTTTTTTTAT
*
24235999 AATTTTTATAAGTTTATATC
1 AATTTTTATAACTTTA-ATC
*
24236019 AATTTTAAT-ACTTTAATC
1 AATTTTTATAACTTTAATC
24236037 -ATTTTTATAA
1 AATTTTTATAA
24236047 TTGTGTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.29
18 4 0.17
19 5 0.21
20 8 0.33
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTTTATAACTTTAATC
Found at i:24236190 original size:11 final size:11
Alignment explanation
Indices: 24236174--24236199 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
24236164 AATATCTATA
24236174 TTTTTTATAAT
1 TTTTTTATAAT
24236185 TTTTTTATAAT
1 TTTTTTATAAT
24236196 TTTT
1 TTTT
24236200 ATAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:24243433 original size:29 final size:31
Alignment explanation
Indices: 24243386--24243446 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
24243376 TGGCCCAAGA
* *
24243386 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATACTCAAAAGTTGAAGGACTAATAGT
*
24243416 GTAAATA-TGAAAAGTTGAAGGACTAATAGT
1 GTAAATACTCAAAAGTTGAAGGACTAATAGT
24243446 G
1 G
24243447 CAACTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (31 bp):
GTAAATACTCAAAAGTTGAAGGACTAATAGT
Found at i:24244155 original size:10 final size:10
Alignment explanation
Indices: 24244140--24244167 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
24244130 TATGTTAGTG
24244140 AAGAGAAAAT
1 AAGAGAAAAT
24244150 AAGAGAAAAT
1 AAGAGAAAAT
24244160 AAGAGAAA
1 AAGAGAAA
24244168 GTGATGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (10 bp):
AAGAGAAAAT
Found at i:24245643 original size:46 final size:46
Alignment explanation
Indices: 24245593--24245959 Score: 567
Period size: 46 Copynumber: 8.0 Consensus size: 46
24245583 GTGTGCTCTC
**
24245593 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATC-
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-CG
**
24245639 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATC-
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-CG
**
24245685 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
*
24245731 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
***
24245777 TGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
*
24245823 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
*** *
24245869 TGACGGGAAATTAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
24245915 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
24245960 ATGACAGAAA
Statistics
Matches: 300, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 299 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:24245989 original size:92 final size:91
Alignment explanation
Indices: 24245607--24246003 Score: 584
Period size: 92 Copynumber: 4.3 Consensus size: 91
24245597 ATGAAATGTG
**
24245607 TAAGACCATGGTTGAAAGATACCATGGCAATC-TGATATGAAATGTGTAAGACCATGGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAA-CGTGATATGAAATGAATAAGACCATGGTTGAAAG
* **
24245671 ATACCATGGCAATC-TGATATG-AAATGTG
65 ATACCATGGCAA-CATGACA-GAAAAT-AA
24245699 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
* *
24245764 TACCATGGCAACATGACGGGAAATGAA
66 TACCATGGCAACATGACAGAAAAT-AA
24245791 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
* *
24245856 TACCATGGCAACATGACGGGAAATTAA
66 TACCATGGCAACATGAC-AGAAAATAA
24245883 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
24245948 TACCATGGCAACATGACAGAAAATAA
66 TACCATGGCAACATGACAGAAAATAA
* * * * *
24245974 GTAATACTATAGTTGAAAGACACTATGGCA
1 -TAAGACCATGGTTGAAAGATACCATGGCA
24246004 TCATGTCAAA
Statistics
Matches: 285, Mismatches: 15, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
91 10 0.04
92 270 0.95
93 5 0.02
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (91 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACAGAAAATAA
Found at i:24245989 original size:138 final size:136
Alignment explanation
Indices: 24245607--24246008 Score: 547
Period size: 138 Copynumber: 2.9 Consensus size: 136
24245597 ATGAAATGTG
**
24245607 TAAGACCATGGTTGAAAGATACCATGGCAATCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAA-CTGATATGAAATGAATAAGACCATGGTTGAAAGA
** * * *
24245672 TACCATGGCAATCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATAT
65 TACCATGGCAA-CTGATATGAAATAAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
24245737 GAAATGAA
129 GAAATGAA
***
24245745 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAAC-TGATATGAAATGAATAAGACCATGGTTGAAAGA
*
24245810 TACCATGGCAACGTGATATGAAATGAA-TAAGACCATGGTTGAAAGATACCATGGCAACATGACG
65 TACCATGGCAAC-TGATATGAAAT-AAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA
*
24245874 GGAAATTAA
128 GGAAATGAA
24245883 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAAC-TGATATGAAATGAATAAGACCATGGTTGAAAGA
* * * * * * *
24245948 TACCATGGCAACATGACA-GAAAATAAGTAATACTATAGTTGAAAGACACTATGGCATCATG
65 TACCATGGCAAC-TGATATG-AAATAAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
24246009 TCAAAGATAA
Statistics
Matches: 235, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
137 5 0.02
138 230 0.98
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (136 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACTGATATGAAATGAATAAGACCATGGTTGAAAGAT
ACCATGGCAACTGATATGAAATAAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGA
AATGAA
Found at i:24246310 original size:16 final size:17
Alignment explanation
Indices: 24246289--24246321 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24246279 ATGATGGAGC
24246289 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
24246305 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
24246322 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:24247876 original size:32 final size:32
Alignment explanation
Indices: 24247837--24247900 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
24247827 GACAACATAT
*
24247837 CTTAGATAATCCTTCGGAGAACAAGCCATCTG
1 CTTAGATAATCCTCCGGAGAACAAGCCATCTG
24247869 CTTAGATAATCCTCCGGAGAACAAGCCATCTG
1 CTTAGATAATCCTCCGGAGAACAAGCCATCTG
24247901 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (32 bp):
CTTAGATAATCCTCCGGAGAACAAGCCATCTG
Found at i:24249411 original size:51 final size:51
Alignment explanation
Indices: 24249323--24249443 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
24249313 ATCACATTTA
* * **
24249323 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATTGCTTG
1 TCACTTGTCACTGATCAGATAAATGTAACTAAAGCTACCACTTATCACTTG
* *
24249374 TCACTTGTCACTGATCAGATAAATGTAACTGAGGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAATGTAACTAAAGCTACCACTTATCACTTG
*
24249425 TCCCTTGTCACTGATCAGA
1 TCACTTGTCACTGATCAGA
24249444 AGTACTCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAATGTAACTAAAGCTACCACTTATCACTTG
Found at i:24258289 original size:85 final size:85
Alignment explanation
Indices: 24258146--24258314 Score: 338
Period size: 85 Copynumber: 2.0 Consensus size: 85
24258136 GTTATTATTA
24258146 TTGTTACTTCACTCTTAGGTTGTCTCATGTAATGCTATTATTATACATGAATGGTTGTGTTCAAA
1 TTGTTACTTCACTCTTAGGTTGTCTCATGTAATGCTATTATTATACATGAATGGTTGTGTTCAAA
24258211 TTGAAATATCAACATTCAAG
66 TTGAAATATCAACATTCAAG
24258231 TTGTTACTTCACTCTTAGGTTGTCTCATGTAATGCTATTATTATACATGAATGGTTGTGTTCAAA
1 TTGTTACTTCACTCTTAGGTTGTCTCATGTAATGCTATTATTATACATGAATGGTTGTGTTCAAA
24258296 TTGAAATATCAACATTCAA
66 TTGAAATATCAACATTCAA
24258315 ATGCTTGGTG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (85 bp):
TTGTTACTTCACTCTTAGGTTGTCTCATGTAATGCTATTATTATACATGAATGGTTGTGTTCAAA
TTGAAATATCAACATTCAAG
Found at i:24258389 original size:25 final size:25
Alignment explanation
Indices: 24258361--24258411 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
24258351 TGAAAATGAA
24258361 TGCCTTTTGCTGTACCTTTGATGTT
1 TGCCTTTTGCTGTACCTTTGATGTT
24258386 TGCCTTTTGCTGTACCTTTGATGTT
1 TGCCTTTTGCTGTACCTTTGATGTT
24258411 T
1 T
24258412 ACTTGACAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.08, C:0.20, G:0.20, T:0.53
Consensus pattern (25 bp):
TGCCTTTTGCTGTACCTTTGATGTT
Found at i:24258572 original size:9 final size:9
Alignment explanation
Indices: 24258528--24258578 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
24258518 CATCAAAGAG
24258528 AAGAGAGAA
1 AAGAGAGAA
*
24258537 GAGAGAAGAGA
1 AAGAG-AGA-A
24258548 AA-AGAGAA
1 AAGAGAGAA
24258556 AA-AGAGAA
1 AAGAGAGAA
24258564 AAGAGAGAA
1 AAGAGAGAA
24258573 AAGAGA
1 AAGAGA
24258579 AAAGAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
8 11 0.30
9 19 0.51
10 5 0.14
11 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (9 bp):
AAGAGAGAA
Found at i:24258577 original size:31 final size:29
Alignment explanation
Indices: 24258528--24258588 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 29
24258518 CATCAAAGAG
*
24258528 AAGAGAGAAGAGAGAAGAGAAAAGAGAAA
1 AAGAGAAAAGAGAGAAGAGAAAAGAGAAA
24258557 AAGAGAAAAGAGAGAAAAGAGAAAAGAGAAA
1 AAGAGAAAAGAGAG--AAGAGAAAAGAGAAA
24258588 A
1 A
24258589 GGGTAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 13 0.45
31 16 0.55
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (29 bp):
AAGAGAAAAGAGAGAAGAGAAAAGAGAAA
Found at i:24258587 original size:7 final size:7
Alignment explanation
Indices: 24258528--24258589 Score: 79
Period size: 7 Copynumber: 8.4 Consensus size: 7
24258518 CATCAAAGAG
*
24258528 AAGAGAG
1 AAGAGAA
*
24258535 AAGAGAG
1 AAGAGAA
24258542 AAGAGAA
1 AAGAGAA
24258549 AAGAGAAA
1 AAGAG-AA
24258557 AAGAGAAA
1 AAGAG-AA
24258565 AGAGAGAA
1 A-AGAGAA
24258573 AAGAGAA
1 AAGAGAA
24258580 AAGAGAA
1 AAGAGAA
24258587 AAG
1 AAG
24258590 GGTAAAAATG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
7 34 0.65
8 14 0.27
9 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (7 bp):
AAGAGAA
Found at i:24258597 original size:16 final size:15
Alignment explanation
Indices: 24258528--24258588 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
24258518 CATCAAAGAG
* *
24258528 AAGAGAGAAGAG-AG
1 AAGAGAAAAGAGAAA
24258542 AAGAGAAAAGAGAAA
1 AAGAGAAAAGAGAAA
24258557 AAGAGAAAAGAGAGAA
1 AAGAGAAAAGAGA-AA
24258573 AAGAGAAAAGAGAAA
1 AAGAGAAAAGAGAAA
24258588 A
1 A
24258589 GGGTAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
14 11 0.26
15 17 0.40
16 15 0.35
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAGAGAAAAGAGAAA
Found at i:24269331 original size:15 final size:15
Alignment explanation
Indices: 24269311--24269343 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
24269301 TAAAGAGTTT
24269311 TAAGTAGATTTTGAG
1 TAAGTAGATTTTGAG
24269326 TAAGTAGATTTTGAG
1 TAAGTAGATTTTGAG
24269341 TAA
1 TAA
24269344 TGGAGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (15 bp):
TAAGTAGATTTTGAG
Found at i:24282519 original size:24 final size:23
Alignment explanation
Indices: 24282489--24282541 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
24282479 TTTCCAATCT
*
24282489 ATATTTTATTT-TAGTTTAATTTAA
1 ATATTTT-TTTATAATTTAATTT-A
24282513 ATATTTTTTTAGTAATTTAATTTA
1 ATATTTTTTTA-TAATTTAATTTA
24282537 ATATT
1 ATATT
24282542 AATTGTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 3 0.12
24 13 0.50
25 10 0.38
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATATTTTTTTATAATTTAATTTA
Found at i:24283246 original size:25 final size:24
Alignment explanation
Indices: 24283216--24283265 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
24283206 TAATATTAGA
*
24283216 TTTAATTTCTAAATTTTTATTATTT
1 TTTAATTTCT-AATTTTAATTATTT
* *
24283241 TTTAATTTGTGATTTTAATTATTT
1 TTTAATTTCTAATTTTAATTATTT
24283265 T
1 T
24283266 ATTTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTAATTTCTAATTTTAATTATTT
Found at i:24285285 original size:20 final size:19
Alignment explanation
Indices: 24285229--24285285 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
24285219 TGTATCTAAT
24285229 ATTAAATAGATAT-TTATTA
1 ATTAAATA-ATATATTATTA
*
24285248 TTTATAA-AATATATTTATTA
1 ATTA-AATAATATA-TTATTA
24285268 ATTAAATAATTATATTAT
1 ATTAAATAA-TATATTAT
24285286 ATGATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.13
19 6 0.19
20 17 0.55
21 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTAAATAATATATTATTA
Found at i:24285488 original size:22 final size:20
Alignment explanation
Indices: 24285446--24285489 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
24285436 AGTAAAAAGA
* *
24285446 AAAAGAAAAAGGAATTAAAT
1 AAAAGAAAAAAGAAATAAAT
24285466 AAAAGAAAGAAAGAAATAGAAT
1 AAAAGAAA-AAAGAAATA-AAT
24285488 AA
1 AA
24285490 GGAACGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAAGAAAAAAGAAATAAAT
Found at i:24285536 original size:14 final size:14
Alignment explanation
Indices: 24285466--24285545 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 14
24285456 GGAATTAAAT
24285466 AAAAGAAA-GAAAG
1 AAAAGAAAGGAAAG
*
24285479 AAATAGAATAAGGAACG
1 AAA-AG-A-AAGGAAAG
*
24285496 AAACAGAGAAGGAAGG
1 AAA-AGA-AAGGAAAG
*
24285512 AAGAG-AA-GAAAG
1 AAAAGAAAGGAAAG
*
24285524 GAAAGAAAGGAAAG
1 AAAAGAAAGGAAAG
24285538 AAAAGAAA
1 AAAAGAAA
24285546 AAGGAAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
12 7 0.13
13 7 0.13
14 14 0.27
15 3 0.06
16 12 0.23
17 9 0.17
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (14 bp):
AAAAGAAAGGAAAG
Found at i:24285969 original size:16 final size:16
Alignment explanation
Indices: 24285931--24285961 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24285921 TAATGTAAAA
24285931 TGAATTG-AAATATAT
1 TGAATTGAAAATATAT
24285946 TGAATTGAAAATATAT
1 TGAATTGAAAATATAT
24285962 ATGATTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
TGAATTGAAAATATAT
Found at i:24288557 original size:13 final size:13
Alignment explanation
Indices: 24288539--24288580 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
24288529 AAACCCTAAA
*
24288539 TTTTCTCCTTTCT
1 TTTTCTTCTTTCT
24288552 TTTTCTTTCTTTCT
1 TTTTC-TTCTTTCT
*
24288566 TTTTATTCTTTCT
1 TTTTCTTCTTTCT
24288579 TT
1 TT
24288581 CCCCTGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTCTTTCT
Found at i:24291154 original size:6 final size:6
Alignment explanation
Indices: 24291143--24291176 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
24291133 AATATTTAAA
24291143 AACTAT AACTAT AACTAT AACTAT AACTACT AAC
1 AACTAT AACTAT AACTAT AACTAT AACTA-T AAC
24291177 ATCGATACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (6 bp):
AACTAT
Found at i:24293488 original size:15 final size:15
Alignment explanation
Indices: 24293439--24293488 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
24293429 TATTTGATAA
24293439 ATTGAAAAAATAAAT
1 ATTGAAAAAATAAAT
* **
24293454 ATTTAAAAAATATCT
1 ATTGAAAAAATAAAT
* *
24293469 GTTGAAAAAGTAAAT
1 ATTGAAAAAATAAAT
24293484 ATTGA
1 ATTGA
24293489 GAGTGTTGAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (15 bp):
ATTGAAAAAATAAAT
Found at i:24295436 original size:24 final size:25
Alignment explanation
Indices: 24295408--24295457 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
24295398 TATACTTTGA
24295408 AATAACAATAA-AATAGTAA-ATAAT
1 AATAACAA-AATAATAGTAATATAAT
24295432 AATAACAAAATAATAGTAATATAAT
1 AATAACAAAATAATAGTAATATAAT
24295457 A
1 A
24295458 GTAAAATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 2 0.08
24 16 0.67
25 6 0.25
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (25 bp):
AATAACAAAATAATAGTAATATAAT
Found at i:24295776 original size:14 final size:14
Alignment explanation
Indices: 24295743--24295787 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
24295733 AAAAATCTTT
*
24295743 TTAATATTTTATAA
1 TTAATTTTTTATAA
24295757 -TAATTTTATTA-AA
1 TTAATTTT-TTATAA
24295770 TTAATTTTTTATAA
1 TTAATTTTTTATAA
24295784 TTAA
1 TTAA
24295788 ATTATTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATTTTTTATAA
Found at i:24295788 original size:19 final size:19
Alignment explanation
Indices: 24295764--24295808 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
24295754 TAATAATTTT
24295764 ATTAAATTAATT-TTTTATA
1 ATTAAATT-ATTGTTTTATA
24295783 ATTAAATTATTGTTTTATA
1 ATTAAATTATTGTTTTATA
24295802 ATATAAA
1 AT-TAAA
24295809 GGTAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTAAATTATTGTTTTATA
Found at i:24297387 original size:25 final size:25
Alignment explanation
Indices: 24297338--24297414 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
24297328 ATATTAAATT
* *
24297338 AATATAATAAACATAAAGGAA-ATAA
1 AATAAAATAAA-ATAAAGAAACATAA
24297363 AATAAAATAAAATAAAGAAACATAA
1 AATAAAATAAAATAAAGAAACATAA
* * **
24297388 GTATAGAA-AAAGGAAAGAAACATAA
1 -AATAAAATAAAATAAAGAAACATAA
24297413 AA
1 AA
24297415 CGAAACAGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
24 9 0.21
25 29 0.67
26 5 0.12
ACGTcount: A:0.70, C:0.04, G:0.10, T:0.16
Consensus pattern (25 bp):
AATAAAATAAAATAAAGAAACATAA
Found at i:24300050 original size:29 final size:28
Alignment explanation
Indices: 24300017--24300090 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
24300007 TGATTGTTTA
* *
24300017 ATTATAAAATATATTATTATTGTTATTAT
1 ATTATAAAATAAATTATTA-TATTATTAT
*
24300046 ATTATAAATTAAATTGATTATATTATTAT
1 ATTATAAAATAAATT-ATTATATTATTAT
*
24300075 ATTATGAAATAAATTA
1 ATTATAAAATAAATTA
24300091 AGAAAAGACA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 34 0.87
30 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
ATTATAAAATAAATTATTATATTATTAT
Found at i:24300219 original size:31 final size:32
Alignment explanation
Indices: 24300148--24300220 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 32
24300138 AAATGAGTAT
*
24300148 ATTTGTATTATTTATATATAATTAGTAAAAAAG
1 ATTTTTATTATTTATATATAATTAG-AAAAAAG
*
24300181 ATGTTTTATTATTTAT-TATTAATTAG-GAAAAG
1 AT-TTTTATTATTTATATA-TAATTAGAAAAAAG
24300213 ATTTTTAT
1 ATTTTTAT
24300221 ATGATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 6 0.17
32 7 0.19
33 4 0.11
34 19 0.53
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (32 bp):
ATTTTTATTATTTATATATAATTAGAAAAAAG
Found at i:24303969 original size:18 final size:19
Alignment explanation
Indices: 24303934--24303972 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
24303924 TGAGTATTGA
24303934 TATTGAATTGAATGAAAATG
1 TATTGAATTG-ATGAAAATG
24303954 TATTGAATTG-TGAAAATG
1 TATTGAATTGATGAAAATG
24303972 T
1 T
24303973 GTGAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
TATTGAATTGATGAAAATG
Found at i:24304192 original size:18 final size:19
Alignment explanation
Indices: 24304157--24304195 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
24304147 TGAGTATTGA
24304157 TATTGAATTGAATGAAAATG
1 TATTGAATTG-ATGAAAATG
24304177 TATTGAATTG-TGAAAATG
1 TATTGAATTGATGAAAATG
24304195 T
1 T
24304196 GTGAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
TATTGAATTGATGAAAATG
Found at i:24304305 original size:223 final size:223
Alignment explanation
Indices: 24303917--24304363 Score: 894
Period size: 223 Copynumber: 2.0 Consensus size: 223
24303907 GGTAAGAGAA
24303917 ATTAAGTTGAGTATTGATATTGAATTGAATGAAAATGTATTGAATTGTGAAAATGTGTGAATATA
1 ATTAAGTTGAGTATTGATATTGAATTGAATGAAAATGTATTGAATTGTGAAAATGTGTGAATATA
24303982 TGGATTGAATATTGATTGAAAGGTGGAAAAATGATTGAATTGAAAATGTGAGAAATTGTGATTGA
66 TGGATTGAATATTGATTGAAAGGTGGAAAAATGATTGAATTGAAAATGTGAGAAATTGTGATTGA
24304047 ATTGAGGTTATATGTGATTTAAATACCCTATTAACTATATCGGGCTGAGTCGGATATAGTTGGCA
131 ATTGAGGTTATATGTGATTTAAATACCCTATTAACTATATCGGGCTGAGTCGGATATAGTTGGCA
24304112 TGCCATAAGATTAGAAGTGTTCAGGGAT
196 TGCCATAAGATTAGAAGTGTTCAGGGAT
24304140 ATTAAGTTGAGTATTGATATTGAATTGAATGAAAATGTATTGAATTGTGAAAATGTGTGAATATA
1 ATTAAGTTGAGTATTGATATTGAATTGAATGAAAATGTATTGAATTGTGAAAATGTGTGAATATA
24304205 TGGATTGAATATTGATTGAAAGGTGGAAAAATGATTGAATTGAAAATGTGAGAAATTGTGATTGA
66 TGGATTGAATATTGATTGAAAGGTGGAAAAATGATTGAATTGAAAATGTGAGAAATTGTGATTGA
24304270 ATTGAGGTTATATGTGATTTAAATACCCTATTAACTATATCGGGCTGAGTCGGATATAGTTGGCA
131 ATTGAGGTTATATGTGATTTAAATACCCTATTAACTATATCGGGCTGAGTCGGATATAGTTGGCA
24304335 TGCCATAAGATTAGAAGTGTTCAGGGAT
196 TGCCATAAGATTAGAAGTGTTCAGGGAT
24304363 A
1 A
24304364 CTTCGACCTC
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
223 224 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (223 bp):
ATTAAGTTGAGTATTGATATTGAATTGAATGAAAATGTATTGAATTGTGAAAATGTGTGAATATA
TGGATTGAATATTGATTGAAAGGTGGAAAAATGATTGAATTGAAAATGTGAGAAATTGTGATTGA
ATTGAGGTTATATGTGATTTAAATACCCTATTAACTATATCGGGCTGAGTCGGATATAGTTGGCA
TGCCATAAGATTAGAAGTGTTCAGGGAT
Found at i:24306072 original size:15 final size:15
Alignment explanation
Indices: 24306048--24306081 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
24306038 GTTCGATAAA
*
24306048 TTGAAAAATTAAGTG
1 TTGAAAAATTAAGAG
*
24306063 TTGAATAATTAAGAG
1 TTGAAAAATTAAGAG
24306078 TTGA
1 TTGA
24306082 GTTTTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TTGAAAAATTAAGAG
Found at i:24306783 original size:125 final size:126
Alignment explanation
Indices: 24306654--24306984 Score: 309
Period size: 128 Copynumber: 2.6 Consensus size: 126
24306644 GGTCAAACGA
*
24306654 AGAAAATCGAAACCCAGCACATTAGGGCACGATCCCTCGAATTTCCAAACA-CAGAAT-ATTGTC
1 AGAAAATCGAAACCCAGCACATTAGGGCACGATCCCTCGAATTTCCAAACATC--AATCATCG-C
* * * ** *
24306717 TTATT-TTTTTGAAG-A-AAAATGTGGACGGAATTTTAAAGGGATGTTTGATTATTTGGACAAAC
63 TT-TTGTTTTTAAAGTAGAAAACGCGGACGGAATTTTAAAGGGAAATTTGATTATTTAGACAAAC
* * *
24306779 AGAAAATCAAAACCTAGCACATTAGGGCACGATTTCC-CGAA-TTCTCAAACATCAATCATCGCT
1 AGAAAATCGAAACCCAGCACATTAGGGCACGA-TCCCTCGAATTTC-CAAACATCAATCATCGCT
* * * *
24306842 TTTGTTTTTAAAGTTTAGAAAACGCGGAGGGGATTTTAAAGGGAAATTTGATTATTTAGATAAAT
64 TTTGTTTTTAAAG--TAGAAAACGCGGACGGAATTTTAAAGGGAAATTTGATTATTTAGACAAAC
* * * * * * * * *
24306907 A-AAAGATTGAAACCCAACACGTTAGGCCACGATCCCTCGAATTTCTAAACATCAAACGTTGCCT
1 AGAAA-ATCGAAACCCAGCACATTAGGGCACGATCCCTCGAATTTCCAAACATCAATCATCGCTT
24306971 TTGTTTTATAAAGT
65 TTGTTTT-TAAAGT
24306985 CAACTCAAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
123 2 0.01
124 17 0.10
125 43 0.26
126 4 0.02
127 8 0.05
128 85 0.51
129 8 0.05
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (126 bp):
AGAAAATCGAAACCCAGCACATTAGGGCACGATCCCTCGAATTTCCAAACATCAATCATCGCTTT
TGTTTTTAAAGTAGAAAACGCGGACGGAATTTTAAAGGGAAATTTGATTATTTAGACAAAC
Found at i:24309811 original size:21 final size:21
Alignment explanation
Indices: 24309762--24309815 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
24309752 TTAAGTTTGG
24309762 TTTATTTCAATTGAGTTTACCT
1 TTTATTTCAATTGAGTTTA-CT
* *
24309784 ATTATTTCAATATGTGTTT-CT
1 TTTATTTCAAT-TGAGTTTACT
24309805 TTTATTTCAAT
1 TTTATTTCAAT
24309816 GTGCTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.43
22 10 0.36
23 6 0.21
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTATTTCAATTGAGTTTACT
Found at i:24317153 original size:99 final size:98
Alignment explanation
Indices: 24316999--24317190 Score: 253
Period size: 99 Copynumber: 1.9 Consensus size: 98
24316989 CCTTTGAGTC
* * * *
24316999 AGTTTGTTGATATAACATTGTGTGATTCTTGCATTTCCTTTTTCTCTTGATAGTATGCTGTTTGT
1 AGTTTGTTGATATAACATTGTATGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
24317064 GCATTAAACAAAAAAGGTTAAAATTTAAAGTGTG
66 GCATTAAACAAAAAA-GTTAAAATTTAAAGTGTG
* * *
24317098 AGTTTGTTGATGTAACATCTG-ATGATTATTGCAATT-CTTTGTTGTCTTTAAAGTATGCTGTTT
1 AGTTTGTTGATATAACAT-TGTATGATTATTGCAATTCCTTT-TTCTCTTGAAAGTATGCTGTTT
* * *
24317161 GTGCATTAAAGAAACAAGTTGAAATTTAAA
64 GTGCATTAAACAAAAAAGTTAAAATTTAAA
24317191 TTTTTGTTAT
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
98 16 0.20
99 63 0.78
100 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (98 bp):
AGTTTGTTGATATAACATTGTATGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
GCATTAAACAAAAAAGTTAAAATTTAAAGTGTG
Found at i:24324235 original size:19 final size:21
Alignment explanation
Indices: 24324211--24324251 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
24324201 CACTTTTTTT
24324211 TATTTAAA-AATAAA-TCAAA
1 TATTTAAATAATAAACTCAAA
*
24324230 TATTTAAATACTAAACTCAAA
1 TATTTAAATAATAAACTCAAA
24324251 T
1 T
24324252 GGTCCATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TATTTAAATAATAAACTCAAA
Found at i:24326655 original size:3 final size:3
Alignment explanation
Indices: 24326649--24326732 Score: 53
Period size: 3 Copynumber: 27.0 Consensus size: 3
24326639 AGGTGCCGGT
* * * * *
24326649 TGA TGA TGT TGA TGA TGA GGC TGA TGA TGA TGA TGA TGA GGT TGA TGAA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG-A
* * *
24326698 TTGAA TGA CGA CT-A CGA TGA TGA TGG TGA TGA TGA
1 -TG-A TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA
24326733 GGACATGTTG
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 54 0.89
4 3 0.05
5 4 0.07
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:24326675 original size:21 final size:21
Alignment explanation
Indices: 24326649--24326696 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
24326639 AGGTGCCGGT
*
24326649 TGATGATGTTGATGATGAGGC
1 TGATGATGATGATGATGAGGC
*
24326670 TGATGATGATGATGATGAGGT
1 TGATGATGATGATGATGAGGC
24326691 TGATGA
1 TGATGA
24326697 ATTGAATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (21 bp):
TGATGATGATGATGATGAGGC
Found at i:24328025 original size:18 final size:18
Alignment explanation
Indices: 24327998--24328039 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 18
24327988 CTATAAAAGC
24327998 TTAATAATTA-TA-TA-T
1 TTAATAATTATTACTATT
24328013 TTAATAATTATTACTATT
1 TTAATAATTATTACTATT
*
24328031 TTTATAATT
1 TTAATAATT
24328040 TTGTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 2 0.09
17 2 0.09
18 9 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATAATTATTACTATT
Found at i:24328200 original size:20 final size:21
Alignment explanation
Indices: 24328168--24328206 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
24328158 TCTTTCATAA
*
24328168 TAATTTATTTAATTTTATTCT
1 TAATTTATTTAATATTATTCT
24328189 TAATTT-TTTAATATTATT
1 TAATTTATTTAATATTATT
24328207 TTTTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (21 bp):
TAATTTATTTAATATTATTCT
Found at i:24332146 original size:17 final size:17
Alignment explanation
Indices: 24332104--24332146 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
24332094 AAAAATATTA
24332104 AGTTTAAAAATAAATTT
1 AGTTTAAAAATAAATTT
* *
24332121 AGATAAAAAATTAAATTT
1 AGTTTAAAAA-TAAATTT
24332139 A-TTTAAAA
1 AGTTTAAAA
24332147 TATGAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AGTTTAAAAATAAATTT
Found at i:24341922 original size:17 final size:17
Alignment explanation
Indices: 24341900--24341934 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
24341890 ATAACATGAA
24341900 AACCATACTTTCTTCAT
1 AACCATACTTTCTTCAT
24341917 AACCATACTTTCTTCAT
1 AACCATACTTTCTTCAT
24341934 A
1 A
24341935 TTTGGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (17 bp):
AACCATACTTTCTTCAT
Found at i:24355263 original size:12 final size:12
Alignment explanation
Indices: 24355248--24355282 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
24355238 GCCAAAACTG
*
24355248 AAGAAGAAGAAC
1 AAGAAGAACAAC
24355260 AAGAAGAACAAC
1 AAGAAGAACAAC
*
24355272 GAGAAGAACAA
1 AAGAAGAACAA
24355283 AAACCCAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAGAACAAC
Found at i:24356123 original size:14 final size:14
Alignment explanation
Indices: 24356104--24356146 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
24356094 TTTTAATAAC
24356104 TTTATTATAGTTTT
1 TTTATTATAGTTTT
24356118 TTTATTATA-TTTGT
1 TTTATTATAGTTT-T
*
24356132 TTTATAATACGTTTT
1 TTTATTATA-GTTTT
24356147 ATCACAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 3 0.12
14 18 0.72
15 1 0.04
16 3 0.12
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTATTATAGTTTT
Found at i:24357223 original size:31 final size:31
Alignment explanation
Indices: 24357188--24357262 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
24357178 TATTTCTTTA
*
24357188 CATATGTATAATTGAATCAAAATCAAAGTTT
1 CATATGTATAATTGAATCAAAATCAAAATTT
* * * * *
24357219 CATATATACATTTGAATTACAATCAAAATTT
1 CATATGTATAATTGAATCAAAATCAAAATTT
24357250 CATATGTATAATT
1 CATATGTATAATT
24357263 ACACCAAATC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (31 bp):
CATATGTATAATTGAATCAAAATCAAAATTT
Found at i:24360360 original size:26 final size:26
Alignment explanation
Indices: 24360325--24360378 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
24360315 CCGCTATATA
24360325 ATAAAAATTTGAGTAATTTCTACATT
1 ATAAAAATTTGAGTAATTTCTACATT
*
24360351 ATAAAAATTTGAGTAATTTCTATATT
1 ATAAAAATTTGAGTAATTTCTACATT
24360377 AT
1 AT
24360379 TGTCTGTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (26 bp):
ATAAAAATTTGAGTAATTTCTACATT
Found at i:24362895 original size:23 final size:23
Alignment explanation
Indices: 24362847--24362895 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
24362837 AAATTTGAAT
* * *
24362847 TTCGAGTTAATCGAATTGAGTTA
1 TTCGAGTCAATCGAATTAAGTAA
24362870 TTCGAGTCAACTCGAA-TAAGTAA
1 TTCGAGTCAA-TCGAATTAAGTAA
24362893 TTC
1 TTC
24362896 AAGTTTCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (23 bp):
TTCGAGTCAATCGAATTAAGTAA
Found at i:24363065 original size:19 final size:19
Alignment explanation
Indices: 24363019--24363106 Score: 61
Period size: 19 Copynumber: 4.3 Consensus size: 19
24363009 AAATTATAAA
24363019 AAAAATATTAAAATAATTTT
1 AAAAAT-TTAAAATAATTTT
* *
24363039 TAATATTTAAAAT-ATTTAT
1 AAAAATTTAAAATAATTT-T
24363058 AAAAATTTCAAAACTTATTTATTTT
1 AAAAATTT-AAAA--TA---ATTTT
* *
24363083 AAAAAATTATAATAATTTT
1 AAAAATTTAAAATAATTTT
24363102 AAAAA
1 AAAAA
24363107 ATCCTAAAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
18 4 0.07
19 24 0.44
20 8 0.15
22 3 0.06
24 3 0.06
25 8 0.15
26 4 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATTTAAAATAATTTT
Found at i:24372143 original size:16 final size:19
Alignment explanation
Indices: 24372104--24372142 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
24372094 AATTTTACTA
24372104 TTTTATTATTAATATATTT
1 TTTTATTATTAATATATTT
24372123 TTTTATT-TT-ATATATTT
1 TTTTATTATTAATATATTT
24372140 TTT
1 TTT
24372143 AAAAGGAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 2 0.10
19 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTATTAATATATTT
Found at i:24373279 original size:6 final size:6
Alignment explanation
Indices: 24373268--24373320 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
24373258 AATTATATGT
* * * *
24373268 TTTTTA TTTTTA TTTTTA GTTTTA GTTTTA GATTTTA GATTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA -TTTTTA TTTTTA
24373318 TTT
1 TTT
24373321 ATTAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 31 0.72
7 12 0.28
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:24380802 original size:21 final size:21
Alignment explanation
Indices: 24380778--24380819 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24380768 TTTTTCTGTT
*
24380778 TTATTTATAAAATAACTAAAA
1 TTATTTATAAAAAAACTAAAA
* *
24380799 TTATTTCTAAAAAAATTAAAA
1 TTATTTATAAAAAAACTAAAA
24380820 AGATAAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TTATTTATAAAAAAACTAAAA
Found at i:24384042 original size:39 final size:40
Alignment explanation
Indices: 24383997--24384168 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
24383987 GCTCCTCGTT
* * *
24383997 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
24384037 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTTGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
24384076 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
24384116 CAAAGGCCTTCGGGGCTTAACCCGAAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCG-GATTTAGTAACTCGCA
24384156 CAAATGCCTTCGG
1 CAAATGCCTTCGG
24384169 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 78 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:24384097 original size:40 final size:39
Alignment explanation
Indices: 24383999--24384221 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
24383989 TCCTCGTTCA
* * * *
24383999 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
24384038 AATGCCTTCGGGACATAACCCGGATTTAATAACTTGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
24384077 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * *
24384117 AAAGGCCTTCGGGGCTTAACCCGAAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCG-GATTTAGTAACTCGCAC
** * * * *
24384157 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
24384198 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
24384222 CAGCATTCAA
Statistics
Matches: 153, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 39 0.25
40 102 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Done.