Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 163 of 187
Found at i:48024938 original size:14 final size:13
Alignment explanation
Indices: 48024919--48024980 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
48024909 TGATTTTGAT
48024919 TTTTTTTCTTTTTG
1 TTTTTTT-TTTTTG
48024933 TTTTTTTTTTTAT-
1 TTTTTTTTTTT-TG
*
48024946 TTTTTTATTTTTG
1 TTTTTTTTTTTTG
48024959 TTTTTTTTATTTTG
1 TTTTTTTT-TTTTG
48024973 ATTTTTTT
1 -TTTTTTT
48024981 GCATTTTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 1 0.02
13 21 0.50
14 13 0.31
15 7 0.17
ACGTcount: A:0.06, C:0.02, G:0.05, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:48024980 original size:1 final size:1
Alignment explanation
Indices: 48024918--48024971 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
48024908 TTGATTTTGA
* * * * * *
48024918 TTTTTTTTCTTTTTGTTTTTTTTTTTATTTTTTTATTTTTGTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48024972 GATTTTTTTG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.06, C:0.02, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:48024987 original size:23 final size:22
Alignment explanation
Indices: 48024938--48025012 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 22
48024928 TTTTGTTTTT
* *
48024938 TTTTTTATTTT-TTTATTTTTGT
1 TTTTTTATTTTGATT-TTTTTGA
48024960 TTTTTTTATTTTGATTTTTTTGCA
1 TTTT-TTATTTTGATTTTTTTG-A
*
48024984 -TTTTCATTTTGACTTTGATTTTGA
1 TTTTTTATTTTGA-TTT--TTTTGA
48025008 TTTTT
1 TTTTT
48025013 CTTTTTCTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
22 12 0.28
23 19 0.44
24 3 0.07
25 9 0.21
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTTATTTTGATTTTTTTGA
Found at i:48029733 original size:22 final size:22
Alignment explanation
Indices: 48029673--48029752 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
48029663 ATATATGTGG
* *
48029673 GTATACATATATAAAGTATAAAA
1 GTATACATATATATA-TATATAA
*
48029696 TTAATACA-A-ATA-ATATATAA
1 GT-ATACATATATATATATATAA
48029716 GTATACATATATATATAT-TAAA
1 GTATACATATATATATATAT-AA
* *
48029738 GTATATAAATATATA
1 GTATACATATATATA
48029753 AGTACGTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.11
20 8 0.17
21 5 0.11
22 22 0.47
23 2 0.04
24 5 0.11
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (22 bp):
GTATACATATATATATATATAA
Found at i:48029755 original size:16 final size:18
Alignment explanation
Indices: 48029705--48029756 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
48029695 ATTAATACAA
48029705 ATAATATATAAGTATACAT
1 ATAATATATAAGTATA-AT
48029724 ATATATATATTAAAGTAT-AT
1 ATA-ATATA-T-AAGTATAAT
48029744 A-AATATATAAGTA
1 ATAATATATAAGTA
48029757 CGTACATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.17
17 1 0.03
18 5 0.17
19 4 0.13
20 8 0.27
21 1 0.03
22 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAATATATAAGTATAAT
Found at i:48032092 original size:22 final size:23
Alignment explanation
Indices: 48032059--48032117 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
48032049 AGAATGATAC
*
48032059 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
48032080 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
48032104 GTGATAAATTTAAA
1 ATGATAAATTTAAA
48032118 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:48036195 original size:10 final size:10
Alignment explanation
Indices: 48036174--48036212 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
48036164 GTGTTTTCTG
*
48036174 TTTTTCAATT
1 TTTTTAAATT
*
48036184 TTTTTAATTT
1 TTTTTAAATT
48036194 TTTTTAAATT
1 TTTTTAAATT
*
48036204 TTCTTAAAT
1 TTTTTAAAT
48036213 CTTTGAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:48036274 original size:16 final size:16
Alignment explanation
Indices: 48036255--48036288 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48036245 ATATCTTTTG
*
48036255 TTATTTTTTTAAAATT
1 TTATTTTTATAAAATT
*
48036271 TTATTTTTATATAATT
1 TTATTTTTATAAAATT
48036287 TT
1 TT
48036289 TCTACATAAT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTTATAAAATT
Found at i:48036326 original size:20 final size:20
Alignment explanation
Indices: 48036269--48036326 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
48036259 TTTTTTAAAA
*
48036269 TTTTATTTTTATAT-AATTT
1 TTTTATATTTATATAAATTT
* * * *
48036288 TTCTACA-TAATATATATTT
1 TTTTATATTTATATAAATTT
48036307 TTTTATATTTATATAAATTT
1 TTTTATATTTATATAAATTT
48036327 GATAAAAGAA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
18 5 0.18
19 13 0.46
20 10 0.36
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATATTTATATAAATTT
Found at i:48036907 original size:19 final size:19
Alignment explanation
Indices: 48036883--48036948 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
48036873 TAAATATATT
48036883 TATTTTTTTAATTTTAAAA
1 TATTTTTTTAATTTTAAAA
**
48036902 TA-TTTTTTACATACTTTTTAA
1 TATTTTTTTA-AT--TTTAAAA
48036923 T-TTTTTTTAAATTTTAAAA
1 TATTTTTTT-AATTTTAAAA
48036942 TATTTTT
1 TATTTTT
48036949 AAAATACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
18 7 0.19
19 10 0.27
20 5 0.14
21 14 0.38
22 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTTTAATTTTAAAA
Found at i:48036937 original size:40 final size:39
Alignment explanation
Indices: 48036884--48036998 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 39
48036874 AAATATATTT
* *
48036884 ATTTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
48036922 ATTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 A-TTTTTTT-AATTTTAAAATATTTTTAAAATAC-TTTTTTA
*
48036964 ATTTTTTTAATTTTAAAATATTTTAAAAATA-TTTT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
48036999 AAAAATACTT
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
38 5 0.07
39 7 0.10
40 44 0.63
41 7 0.10
42 7 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:48036948 original size:11 final size:11
Alignment explanation
Indices: 48036934--48037036 Score: 69
Period size: 11 Copynumber: 9.9 Consensus size: 11
48036924 TTTTTTTAAA
48036934 TTTTAAAATAT
1 TTTTAAAATAT
48036945 TTTTAAAATACT
1 TTTTAAAATA-T
**
48036957 TTTTTTAAT-T
1 TTTTAAAATAT
*
48036967 TTTT----TAA
1 TTTTAAAATAT
48036974 TTTTAAAATAT
1 TTTTAAAATAT
*
48036985 TTTAAAAATAT
1 TTTTAAAATAT
*
48036996 TTTAAAAATACT
1 TTTTAAAATA-T
**
48037008 TTTTTTAAT-T
1 TTTTAAAATAT
48037018 TTTT-AAA-AT
1 TTTTAAAATAT
48037027 TTTTAAAATA
1 TTTTAAAATA
48037037 AAAATGGGCC
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
9 7 0.10
10 13 0.18
11 33 0.45
12 15 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:48036960 original size:51 final size:49
Alignment explanation
Indices: 48036894--48037011 Score: 123
Period size: 51 Copynumber: 2.3 Consensus size: 49
48036884 ATTTTTTTAA
* **
48036894 TTTTAAAATATTTTTTACATACTTTTTAATTTTTTTTAA-ATTTT-AAAATAT
1 TTTTAAAATACTTTTTA-AT-CTTTTTAA--TTTTAAAATATTTTAAAAATAT
*
48036945 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTAAAAATAT
1 TTTTAAAATAC--TTTTTAATCTTTTTAATTTTAAAATATTTTAAAAATAT
*
48036996 TTTAAAAATACTTTTT
1 TTTTAAAATACTTTTT
48037012 TTAATTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
49 11 0.19
50 5 0.09
51 34 0.59
52 2 0.03
53 6 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (49 bp):
TTTTAAAATACTTTTTAATCTTTTTAATTTTAAAATATTTTAAAAATAT
Found at i:48037012 original size:51 final size:52
Alignment explanation
Indices: 48036933--48037036 Score: 167
Period size: 51 Copynumber: 2.0 Consensus size: 52
48036923 TTTTTTTTAA
* *
48036933 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTT-TAA-TTTTAAAAT
1 ATTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAAT
48036983 ATTTTAAAAATATTTTAAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAAT
1 ATTTT-AAAATATTTTAAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAAT
48037036 A
1 A
48037037 AAAATGGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
50 5 0.10
51 32 0.65
52 2 0.04
53 10 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (52 bp):
ATTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAAT
Found at i:48040607 original size:23 final size:22
Alignment explanation
Indices: 48040581--48040626 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
48040571 TGTAACTTTG
* *
48040581 TATTTGTCTGATTTATGATTTCT
1 TATTTGTCTAATTT-GGATTTCT
*
48040604 TATTTTTCTAATTTGGATTTCT
1 TATTTGTCTAATTTGGATTTCT
48040626 T
1 T
48040627 TCCTAATCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (22 bp):
TATTTGTCTAATTTGGATTTCT
Found at i:48044548 original size:15 final size:15
Alignment explanation
Indices: 48044528--48044562 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
48044518 GGTTTGTCTC
48044528 TTTGTTTGTTTTTA-T
1 TTTGTTT-TTTTTACT
48044543 TTTGTTTTTTTTACT
1 TTTGTTTTTTTTACT
48044558 TTTGT
1 TTTGT
48044563 CTCTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.06, C:0.03, G:0.11, T:0.80
Consensus pattern (15 bp):
TTTGTTTTTTTTACT
Found at i:48048869 original size:45 final size:45
Alignment explanation
Indices: 48048805--48048896 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
48048795 TTAATGCACA
48048805 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
1 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
48048850 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
1 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
48048895 CT
1 CT
48048897 GATTTGAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (45 bp):
CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
Found at i:48051820 original size:32 final size:32
Alignment explanation
Indices: 48051776--48051848 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
48051766 AGCTACAAGA
*
48051776 ATGGA-AGTGCTACATTGCATCAAGGATACCG
1 ATGGATAGAGCTACATTGCATCAAGGATACCG
*
48051807 ATGGATAGAGCTACATTGGATCAAGGATACCG
1 ATGGATAGAGCTACATTGCATCAAGGATACCG
48051839 ATGGATAGAG
1 ATGGATAGAG
48051849 ACTTTCCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 5 0.13
32 34 0.87
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (32 bp):
ATGGATAGAGCTACATTGCATCAAGGATACCG
Found at i:48052398 original size:45 final size:45
Alignment explanation
Indices: 48052334--48052500 Score: 307
Period size: 45 Copynumber: 3.7 Consensus size: 45
48052324 GCCATATCCT
*
48052334 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
*
48052379 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATACCCTTCTTCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
48052424 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
*
48052469 TCTTCCTCGGATCTACCATAACTTGGTTTCCT
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCT
48052501 CTCATACCCG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 118 1.00
ACGTcount: A:0.16, C:0.35, G:0.10, T:0.39
Consensus pattern (45 bp):
TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
Found at i:48052815 original size:54 final size:54
Alignment explanation
Indices: 48052752--48052863 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
48052742 TGTTCGCCAT
* *
48052752 ATTCGGGTCTCCGGCCATGCCCAGATT-CAAATTCAGGAGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAG-TTCCAAACTCAGGAGGCGGAGGCTGCTCAA
* * *
48052806 ATTCGGGTCTCCGTCGATACCCAGTTCCAAACTCAGGCGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
48052860 ATTC
1 ATTC
48052864 TGATCTACGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
53 2 0.04
54 50 0.96
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.21
Consensus pattern (54 bp):
ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
Found at i:48054029 original size:21 final size:19
Alignment explanation
Indices: 48054004--48054058 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 19
48053994 TGCGACATAC
*
48054004 CAACTAAATATTTAACATTGT
1 CAACTAAATATTTAA-A-TAT
*
48054025 TAACTTAAAATATTTAAATAT
1 CAAC-T-AAATATTTAAATAT
48054046 CAACTAAATATTT
1 CAACTAAATATTT
48054059 TTAGACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.28
20 1 0.03
21 8 0.28
22 2 0.07
23 10 0.34
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (19 bp):
CAACTAAATATTTAAATAT
Found at i:48056121 original size:15 final size:16
Alignment explanation
Indices: 48056092--48056121 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48056082 TGTGTTTACG
48056092 TTTTCGGGTTCTTTAT
1 TTTTCGGGTTCTTTAT
48056108 TTTTCGGGTT-TTTA
1 TTTTCGGGTTCTTTA
48056122 GGTTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.07, C:0.10, G:0.20, T:0.63
Consensus pattern (16 bp):
TTTTCGGGTTCTTTAT
Found at i:48058676 original size:30 final size:30
Alignment explanation
Indices: 48058642--48058746 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
48058632 AATGTGACCA
48058642 ATTACAGGCTATGACAGGTAAATGCAAATG
1 ATTACAGGCTATGACAGGTAAATGCAAATG
** ***
48058672 ATTACAAGG-TATGA-AAATAAAAATG-TGTTCG
1 ATTAC-AGGCTATGACAGGT--AAATGCAAAT-G
48058703 ATTACAGGCTATGACAGGTAAATGCAAATG
1 ATTACAGGCTATGACAGGTAAATGCAAATG
* *
48058733 ATTGCAGGGTATGA
1 ATTACAGGCTATGA
48058747 TAATGCAAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 2 0.04
30 32 0.57
31 20 0.36
32 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (30 bp):
ATTACAGGCTATGACAGGTAAATGCAAATG
Found at i:48058713 original size:61 final size:61
Alignment explanation
Indices: 48058613--48058746 Score: 223
Period size: 61 Copynumber: 2.2 Consensus size: 61
48058603 TAGTACAGTG
48058613 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
* ** *
48058674 TACAAGGTATGAAAATAAAAATGTGTTCGATTACAGGCTATGACAGGTAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
*
48058735 TGCAGGGTATGA
1 TACAGGGTATGA
48058747 TAATGCAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (61 bp):
TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
Found at i:48070710 original size:13 final size:13
Alignment explanation
Indices: 48070692--48070718 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48070682 ATATATTTTT
48070692 AGATTTAAAATTA
1 AGATTTAAAATTA
48070705 AGATTTAAAATTA
1 AGATTTAAAATTA
48070718 A
1 A
48070719 CAATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AGATTTAAAATTA
Found at i:48077036 original size:12 final size:11
Alignment explanation
Indices: 48077024--48077063 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
48077014 TTTCTTTAAT
48077024 TTTCTCTCAAA
1 TTTCTCTCAAA
*
48077035 TTTATCTCAAA
1 TTTCTCTCAAA
48077046 TTTCTCTCTAAA
1 TTTCTCTC-AAA
48077058 TTTCTC
1 TTTCTC
48077064 AAAGCTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:48077072 original size:21 final size:22
Alignment explanation
Indices: 48077026--48077073 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
48077016 TCTTTAATTT
**
48077026 TCTCTCAAATTTATCTCAAATT
1 TCTCTCAAATTTATCTCAAAGC
48077048 TCTCTCTAAA-TT-TCTCAAAGC
1 TCTCTC-AAATTTATCTCAAAGC
48077069 TCTCT
1 TCTCT
48077074 TTACTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.52
22 8 0.35
23 3 0.13
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTATCTCAAAGC
Found at i:48080024 original size:33 final size:32
Alignment explanation
Indices: 48079983--48080066 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 32
48079973 ACTTGAGTTG
* *
48079983 GGAGGAGTGTTGTATTGTGGTAGATACGACCC
1 GGAGGAGTGCTGTATTGCGGTAGATACGACCC
** * **
48080015 AGGAGGAGTGGAGTAATGCGGTAGATACGGGCC
1 -GGAGGAGTGCTGTATTGCGGTAGATACGACCC
48080048 GAGAGGAGTGCTGTATTGC
1 G-GAGGAGTGCTGTATTGC
48080067 AGTGGTACTA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 1 0.02
33 40 0.98
ACGTcount: A:0.24, C:0.12, G:0.42, T:0.23
Consensus pattern (32 bp):
GGAGGAGTGCTGTATTGCGGTAGATACGACCC
Found at i:48089550 original size:16 final size:16
Alignment explanation
Indices: 48089521--48089566 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
48089511 ATAAAGTTTC
* *
48089521 ACTGGAATGGAATAAT
1 ACTGTAATGGAATAAA
* *
48089537 ATTGTAATGAAATAAA
1 ACTGTAATGGAATAAA
48089553 ACTGTAATGGAATA
1 ACTGTAATGGAATA
48089567 GAGTTGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (16 bp):
ACTGTAATGGAATAAA
Found at i:48089608 original size:46 final size:44
Alignment explanation
Indices: 48089555--48089645 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 44
48089545 GAAATAAAAC
**
48089555 TGTAATGGAATAGAGTTGTAATCAGTGATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAAT-AGT-ATT-AATGTGTTTGGTTGAA
* *
48089601 TGTAATGGAATATAACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
48089645 T
1 T
48089646 AAAATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 16 0.40
45 3 0.08
46 19 0.47
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (44 bp):
TGTAATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
Found at i:48096088 original size:10 final size:11
Alignment explanation
Indices: 48096069--48096098 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
48096059 AATGACACGG
48096069 GAAGAAAAAAA
1 GAAGAAAAAAA
48096080 GAA-AAAAAAA
1 GAAGAAAAAAA
48096090 GAAGAAAAA
1 GAAGAAAAA
48096099 CTCCAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
GAAGAAAAAAA
Found at i:48113808 original size:20 final size:21
Alignment explanation
Indices: 48113771--48113809 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
48113761 ATTAATGTTA
48113771 GATTAAATTTAATATTAAAGT
1 GATTAAATTTAATATTAAAGT
48113792 GATT-AATTT-ATAGTTAAA
1 GATTAAATTTAATA-TTAAA
48113810 TTCTCTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
GATTAAATTTAATATTAAAGT
Found at i:48116340 original size:26 final size:26
Alignment explanation
Indices: 48116308--48116366 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
48116298 TATTTTCTCG
48116308 AAATTTTACCAGGGGCAAAATCGATA
1 AAATTTTACCAGGGGCAAAATCGATA
* * * *
48116334 AAGTTTTACCATGGGTAAAATCGTTA
1 AAATTTTACCAGGGGCAAAATCGATA
48116360 AAATTTT
1 AAATTTT
48116367 GCTAGAGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCGATA
Found at i:48121066 original size:25 final size:24
Alignment explanation
Indices: 48121038--48121086 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
48121028 ATCCAAAATA
48121038 CTAAAAACATT-AAAATAAATGTTTT
1 CTAAAAA-ATTGAAAATAAAT-TTTT
*
48121063 CTAACAAATTGAAAATAAATTTTT
1 CTAAAAAATTGAAAATAAATTTTT
48121087 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
CTAAAAAATTGAAAATAAATTTTT
Found at i:48122662 original size:9 final size:9
Alignment explanation
Indices: 48122633--48122669 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
48122623 TGAGTTTTCA
48122633 AATTCGAAT
1 AATTCGAAT
*
48122642 AACTCGAAT
1 AATTCGAAT
48122651 AATTCGAAT
1 AATTCGAAT
*
48122660 AATTTGAAT
1 AATTCGAAT
48122669 A
1 A
48122670 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48123083 original size:16 final size:16
Alignment explanation
Indices: 48123059--48123096 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
48123049 TTTGGTTCGC
* *
48123059 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
48123075 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
48123091 TGTAAT
1 TGTAAT
48123097 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:48123180 original size:39 final size:43
Alignment explanation
Indices: 48123075--48123184 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
48123065 GGATTAGAGG
48123075 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
48123120 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
48123160 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
48123185 TAATAGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:48123351 original size:18 final size:17
Alignment explanation
Indices: 48123330--48123364 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48123320 TTATTATTAA
*
48123330 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48123348 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48123365 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48123418 original size:157 final size:156
Alignment explanation
Indices: 48123217--48123532 Score: 569
Period size: 157 Copynumber: 2.0 Consensus size: 156
48123207 TAGAATACCC
* *
48123217 TTAGCATAAATTTGTTTTGGTAAGTGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
48123282 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAA-ATAATTATTATTAAATATATTATAATTAAAA
*
48123347 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTATTAATAA
*
48123374 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
48123439 ATATCAATAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAAT
66 ATATCAATAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAAT
48123504 ATATAATTTAATAAAATTATTAATAA
131 ATATAATTTAATAAAATTATTAATAA
48123530 TTA
1 TTA
48123533 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
156 59 0.39
157 94 0.61
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTATTAATAA
Found at i:48123485 original size:15 final size:16
Alignment explanation
Indices: 48123467--48123533 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
48123457 TTAATCATAT
*
48123467 TTAAAATA-ATTATTA
1 TTAAAATATATTATAA
48123482 TT-AAATATATTATAA
1 TTAAAATATATTATAA
*
48123497 TTAAAATATATAATTTAA
1 TTAAAATATAT--TATAA
48123515 -TAAAAT-TATTAATAA
1 TTAAAATATATT-ATAA
48123530 TTAA
1 TTAA
48123534 TATTCTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
14 6 0.14
15 13 0.30
16 14 0.33
17 6 0.14
18 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:48123507 original size:18 final size:18
Alignment explanation
Indices: 48123486--48123533 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
48123476 TTATTATTAA
48123486 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
48123504 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
48123521 -TAT-TAATAATTAA
1 ATATATTATAATTAA
48123534 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:48123514 original size:14 final size:15
Alignment explanation
Indices: 48123470--48123516 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
48123460 ATCATATTTA
*
48123470 AAATA-ATTATTATT
1 AAATATATTATAATT
48123484 AAATATATTATAATT
1 AAATATATTATAATT
48123499 AAA-ATA-TATAATT
1 AAATATATTATAATT
*
48123512 TAATA
1 AAATA
48123517 AAATTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.31
14 9 0.31
15 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATATTATAATT
Found at i:48123515 original size:75 final size:74
Alignment explanation
Indices: 48123283--48123516 Score: 170
Period size: 75 Copynumber: 3.0 Consensus size: 74
48123273 AGATTATTAT
48123283 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
1 TATCAATAATAAATAATTTAATCATATTTAAA-ATAATTATTATTAAATATA-TTTAATTAAAAT
48123348 ATATAATTTAA
64 ATATAATTTAA
* ** * * * * * * * * *
48123359 TA-AAATTCTTAATAATTAGCAGAAAT-TTGTTTTGGTAAATTATTATTGTT-ATTGTTATTTAA
1 TATCAATAATAAATAATT-----TAATCAT-ATTT--AAAATAATTATTATTAAAT-ATATTT-A
** * *
48123421 ATTTTAATA-AGATTATTAA
56 ATTAAAATATATAAT-TTAA
48123440 TATCAATAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAATA
1 TATCAATAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATT-TAATTAAAATA
48123505 TATAATTTAA
65 TATAATTTAA
48123515 TA
1 TA
48123517 AAATTATTAA
Statistics
Matches: 110, Mismatches: 32, Indels: 33
0.63 0.18 0.19
Matches are distributed among these distances:
75 41 0.37
76 8 0.07
77 6 0.05
78 1 0.01
79 1 0.01
80 14 0.13
81 26 0.24
82 13 0.12
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (74 bp):
TATCAATAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTTAATTAAAATAT
ATAATTTAA
Found at i:48123528 original size:78 final size:78
Alignment explanation
Indices: 48123289--48123534 Score: 200
Period size: 78 Copynumber: 3.1 Consensus size: 78
48123279 TTATTATCAA
*
48123289 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAA-ATAATTATTATTAAATATATTATAATTAAAATATATAA
*
48123354 TTTAATAAAATTCT
65 TTTAATAAAATTAT
* ** * * * * * * * *
48123368 TAATAATTAGCA-GAAAT-TTGTTTTGGTAAATTATTATTGTT--AT-TGTTAT--TTAAATTTT
1 TAATAAATA--ATTTAATCAT-ATTT--AAAATAATTATTATTAAATATATTATAATTAAAATAT
* * * * *
48123426 AATAAGATTATTAATATCAA
61 -ATAA-TTTAATAAAATTAT
48123446 TAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAAT
1 TAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAAT
48123511 TTAATAAAATTAT
66 TTAATAAAATTAT
*
48123524 TAATAATTAAT
1 TAATAAATAAT
48123535 ATTCTTATAT
Statistics
Matches: 118, Mismatches: 35, Indels: 29
0.65 0.19 0.16
Matches are distributed among these distances:
75 12 0.10
76 8 0.07
77 12 0.10
78 45 0.38
79 15 0.13
80 13 0.11
81 11 0.09
82 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (78 bp):
TAATAAATAATTTAATCATATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAAT
TTAATAAAATTAT
Found at i:48123568 original size:61 final size:61
Alignment explanation
Indices: 48123501--48123688 Score: 194
Period size: 61 Copynumber: 3.1 Consensus size: 61
48123491 TTATAATTAA
48123501 AATATATAATTTAATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * *
48123562 AATATATGATACTGTAA-AATATAAATTAA-AA-TAATAATTATTAAAT--ATATTA-T--AATT
1 AATATAT-A-A-TTTAATAAAAT-TATTAATAATTAAT-ATTCTTATATGAAT-TTACTCAAATC
*
48123619 AA
60 AT
*
48123621 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
48123682 AATATAT
1 AATATAT
48123689 GATACTATAA
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
56 8 0.08
57 15 0.15
58 8 0.08
59 14 0.14
61 21 0.21
62 8 0.08
63 15 0.15
64 9 0.09
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:48123597 original size:156 final size:154
Alignment explanation
Indices: 48123269--48123587 Score: 365
Period size: 156 Copynumber: 2.0 Consensus size: 154
48123259 TTTAAATTTT
*
48123269 AATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
1 AATAAGA-TATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
* * * * * * **
48123334 ATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAAT
65 ATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAACACAAATATGATTTACTAAAT
* * * * *
48123399 TATTATTGTTATTGTTATTTAAATTTT
130 TAATATTGATACTGTTA--TAAATATA
48123426 AATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAA-ATAATTATTATTAAATAT
1 AATAAGA-TATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
* **
48123490 ATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAATATTCTTATATGAATTTACTC
65 ATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAACA--CAAATATG-ATTTACT-
48123555 AAATCATAATATATGATACTG-TA-AAATATA
126 AAAT--TAATAT-TGATACTGTTATAAATATA
48123585 AAT
1 AAT
48123588 TAAAATAATA
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
156 60 0.43
157 45 0.33
158 4 0.03
159 12 0.09
160 4 0.03
162 7 0.05
163 6 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (154 bp):
AATAAGATATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
TTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAACACAAATATGATTTACTAAATT
AATATTGATACTGTTATAAATATA
Found at i:48123602 original size:120 final size:120
Alignment explanation
Indices: 48123465--48123761 Score: 490
Period size: 120 Copynumber: 2.5 Consensus size: 120
48123455 ATTTAATCAT
*
48123465 ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
1 ATTTAAAATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
* *
48123530 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
48123586 A-TTAAAATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAAAATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
48123650 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * * *
48123705 ATTTGAAATAATTAA-TATTAAATATATTTTAATTAAGATATATGATTTAATAAAATT
1 ATTTAAAATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
48123762 TAAAATAATT
Statistics
Matches: 166, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 3 0.02
120 159 0.96
121 4 0.02
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (120 bp):
ATTTAAAATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:48123625 original size:16 final size:16
Alignment explanation
Indices: 48123585--48123630 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
48123575 GTAAAATATA
48123585 AATTAAAATA-ATAAT
1 AATTAAAATATATAAT
* *
48123600 TATT-AAATATATTAT
1 AATTAAAATATATAAT
48123615 AATTAAAATATATAAT
1 AATTAAAATATATAAT
48123631 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 5 0.20
15 10 0.40
16 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAAATATATAAT
Found at i:48123863 original size:54 final size:51
Alignment explanation
Indices: 48123702--48123863 Score: 120
Period size: 54 Copynumber: 3.1 Consensus size: 51
48123692 ACTATAAAAG
* * * *
48123702 AAAATTTGAAATAATTAA-TATTAAATATATTTTAATTAAGATATATGATTTAAT
1 AAAATTTAAAATAA-TAATTATT-AATATAATTTAA-TAATATATATAATTT-AT
* * * * *
48123756 AAAATTTAAAATAATTATAACTAATA-AA-TT-AT-AT-TTTATGAATTTGT
1 AAAATTTAAAATAATAATTATTAATATAATTTAATAATATATAT-AATTTAT
*
48123803 ATAATTTAAAATAATAATTATTACATATAATTTAATAATAATATATAATTTCAT
1 AAAATTTAAAATAATAATTATTA-ATATAATTTAATAAT-ATATATAATTT-AT
48123857 AAAATTT
1 AAAATTT
48123864 GTGATAATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
47 24 0.29
48 8 0.10
49 3 0.04
50 3 0.04
51 4 0.05
52 3 0.04
53 11 0.13
54 26 0.32
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (51 bp):
AAAATTTAAAATAATAATTATTAATATAATTTAATAATATATATAATTTAT
Found at i:48123872 original size:91 final size:91
Alignment explanation
Indices: 48123777--48123984 Score: 269
Period size: 91 Copynumber: 2.3 Consensus size: 91
48123767 TAATTATAAC
* * * *
48123777 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
48123841 TAATATATAATTTCATAAAATTTGTGA
65 TAATATATAATTTCATAAAATTTGTGA
* * *
48123868 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
48123933 GATATATAATTTCATAAAATTCT-TAA
66 AATATATAATTTCATAAAATT-TGTGA
*
48123959 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
48123985 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
91 80 0.77
92 23 0.22
93 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTTGTGA
Found at i:48125530 original size:14 final size:15
Alignment explanation
Indices: 48125497--48125530 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
48125487 AGTGTTCATC
*
48125497 CAAAACAGAACCATA
1 CAAAACAGAAACATA
48125512 CAAAACAGAAACA-A
1 CAAAACAGAAACATA
48125526 CAAAA
1 CAAAA
48125531 TCTGCTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.68, C:0.24, G:0.06, T:0.03
Consensus pattern (15 bp):
CAAAACAGAAACATA
Found at i:48126440 original size:9 final size:9
Alignment explanation
Indices: 48126426--48126454 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
48126416 AATTTCACAT
48126426 TTTATATTA
1 TTTATATTA
48126435 TTTATATTA
1 TTTATATTA
48126444 TTTATATTA
1 TTTATATTA
48126453 TT
1 TT
48126455 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:48126831 original size:5 final size:5
Alignment explanation
Indices: 48126821--48126846 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
48126811 GAACAAATAT
48126821 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
48126847 ATTTCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:48126946 original size:5 final size:5
Alignment explanation
Indices: 48126936--48126966 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
48126926 CTCGAAAATT
48126936 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
48126967 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:48128945 original size:14 final size:14
Alignment explanation
Indices: 48128926--48128961 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48128916 TTTATGAACT
48128926 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
48128940 TTTTTA-TTTTTAA
1 TTTTTATTTTTTAA
48128953 TTATTTATT
1 TT-TTTATT
48128962 GATATGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 10 0.50
15 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTTTTAA
Found at i:48130056 original size:88 final size:89
Alignment explanation
Indices: 48129960--48130131 Score: 240
Period size: 88 Copynumber: 1.9 Consensus size: 89
48129950 ACTTTTTTAT
* * *
48129960 ACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGGCTCTCAA-ACTT-AAAAAAAACAA
1 ACTCAATTGAGTACTTAAACTGTCAAAATGCATCAAAAAGGCTCTCAAGACTTCAAAAAAAACAA
48130023 TTAAGTCCTGTTTTTTTTTTTTTGC
66 TTAAGTCCT-TTTTTTTTTTTTTGC
* ** *
48130048 ACTCAATTGAGTATTTAAACTGTCAAAATGCATCAAAAAGGCTCTCAAGGTTTTTCAAAAAAAGC
1 ACTCAATTGAGTACTTAAACTGTCAAAATGCATCAAAAAGGCTCTCAA-G-ACTTCAAAAAAAAC
48130113 AATTAAGTCCTTTTTTTTT
64 AATTAAGTCCTTTTTTTTT
48130132 GCACTCAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
88 44 0.60
91 10 0.14
92 19 0.26
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (89 bp):
ACTCAATTGAGTACTTAAACTGTCAAAATGCATCAAAAAGGCTCTCAAGACTTCAAAAAAAACAA
TTAAGTCCTTTTTTTTTTTTTTGC
Found at i:48130273 original size:10 final size:9
Alignment explanation
Indices: 48130234--48130384 Score: 78
Period size: 9 Copynumber: 16.4 Consensus size: 9
48130224 GACATGCAAA
*
48130234 AAAAAATAT
1 AAAAATTAT
48130243 AAAAA-T-T
1 AAAAATTAT
*
48130250 AAAAATCAGT
1 AAAAATTA-T
*
48130260 AAAAGTTAT
1 AAAAATTAT
48130269 AAAAATTAT
1 AAAAATTAT
*
48130278 AAAAATTTTT
1 AAAAA-TTAT
***
48130288 AATTTTTAAT
1 AAAAATT-AT
48130298 AAAAA-TATT
1 AAAAATTA-T
*
48130307 AAAATTTTATT
1 AAAA-ATTA-T
* *
48130318 GAAAACTAT
1 AAAAATTAT
48130327 AAAAA-TAT
1 AAAAATTAT
*
48130335 AAAAATCAT
1 AAAAATTAT
48130344 AAAAA-TAT
1 AAAAATTAT
*
48130352 AAAATTTTAT
1 AAAA-ATTAT
*
48130362 AAAAATCAT
1 AAAAATTAT
48130371 AAAAAATTAT
1 -AAAAATTAT
48130381 AAAA
1 AAAA
48130385 TGCATAAAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
7 6 0.06
8 16 0.15
9 46 0.43
10 32 0.30
11 7 0.07
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:48130282 original size:19 final size:18
Alignment explanation
Indices: 48130234--48130384 Score: 78
Period size: 19 Copynumber: 8.2 Consensus size: 18
48130224 GACATGCAAA
*
48130234 AAAAAATATAAAAA-T-T
1 AAAAATTATAAAAATTAT
* *
48130250 AAAAATCAGTAAAAGTTAT
1 AAAAATTA-TAAAAATTAT
*
48130269 AAAAATTATAAAAATTTTT
1 AAAAATTATAAAAA-TTAT
***
48130288 AATTTTTAATAAAAA-TATT
1 AAAAATT-ATAAAAATTA-T
* * *
48130307 AAAATTTTATTGAAAACTAT
1 AAAA-ATTA-TAAAAATTAT
*
48130327 AAAAA-TATAAAAATCAT
1 AAAAATTATAAAAATTAT
*
48130344 AAAAA-TATAAAATTTTAT
1 AAAAATTATAAAA-ATTAT
*
48130362 AAAAATCATAAAAAATTAT
1 AAAAATTAT-AAAAATTAT
48130381 AAAA
1 AAAA
48130385 TGCATAAAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 21
0.71 0.15 0.15
Matches are distributed among these distances:
16 6 0.06
17 24 0.24
18 17 0.17
19 29 0.28
20 24 0.24
21 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:48130314 original size:20 final size:20
Alignment explanation
Indices: 48130276--48130315 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
48130266 TATAAAAATT
* * *
48130276 ATAAAAATTTTTAATTTTTA
1 ATAAAAATATTAAAATTTTA
48130296 ATAAAAATATTAAAATTTTA
1 ATAAAAATATTAAAATTTTA
48130316 TTGAAAACTA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATATTAAAATTTTA
Found at i:48130330 original size:8 final size:8
Alignment explanation
Indices: 48130319--48130375 Score: 60
Period size: 8 Copynumber: 6.6 Consensus size: 8
48130309 AATTTTATTG
*
48130319 AAAACTAT
1 AAAAATAT
48130327 AAAAATAT
1 AAAAATAT
48130335 AAAAATCAT
1 AAAAAT-AT
48130344 AAAAATAT
1 AAAAATAT
*
48130352 AAAATTTTAT
1 AAAA--ATAT
48130362 AAAAATCAT
1 AAAAAT-AT
48130371 AAAAA
1 AAAAA
48130376 ATTATAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 20 0.48
9 15 0.36
10 7 0.17
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:48130350 original size:46 final size:46
Alignment explanation
Indices: 48130296--48130394 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
48130286 TTAATTTTTA
*
48130296 ATAAAAATATTAAAATTTTATTGAAAA-C-TATAAAAA-TATAAAAAT-C
1 ATAAAAATA-TAAAATTTTA-TAAAAATCATA-AAAAATTAT-AAAATGC
48130342 ATAAAAATATAAAATTTTATAAAAATCATAAAAAATTATAAAATGC
1 ATAAAAATATAAAATTTTATAAAAATCATAAAAAATTATAAAATGC
48130388 ATAAAAA
1 ATAAAAA
48130395 GACCCTTAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
44 5 0.10
45 21 0.44
46 22 0.46
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (46 bp):
ATAAAAATATAAAATTTTATAAAAATCATAAAAAATTATAAAATGC
Found at i:48130369 original size:27 final size:29
Alignment explanation
Indices: 48130332--48130385 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
48130322 ACTATAAAAA
48130332 TATAAAAATCAT-AAAAA-TATAAAATTT
1 TATAAAAATCATAAAAAATTATAAAATTT
48130359 TATAAAAATCATAAAAAATTATAAAAT
1 TATAAAAATCATAAAAAATTATAAAAT
48130386 GCATAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 12 0.48
28 5 0.20
29 8 0.32
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (29 bp):
TATAAAAATCATAAAAAATTATAAAATTT
Found at i:48130390 original size:19 final size:19
Alignment explanation
Indices: 48130319--48130394 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
48130309 AATTTTATTG
*
48130319 AAAACTATAAAAAT-AT-A
1 AAAATTATAAAAATCATAA
*
48130336 AAAATCATAAAAAT-ATAA
1 AAAATTATAAAAATCATAA
**
48130354 AATTTTATAAAAATCATAA
1 AAAATTATAAAAATCATAA
48130373 AAAATTAT-AAAATGCATAA
1 AAAATTATAAAAAT-CATAA
48130392 AAA
1 AAA
48130395 GACCCTTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
17 14 0.29
18 17 0.35
19 18 0.37
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.26
Consensus pattern (19 bp):
AAAATTATAAAAATCATAA
Found at i:48130663 original size:20 final size:21
Alignment explanation
Indices: 48130592--48130669 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 21
48130582 TTACAAATTT
*
48130592 TATATTTCTTTATATTTTTTA
1 TATATTTCTATATATTTTTTA
* **
48130613 TA-ATTTTCT-TACA-ACTTTA
1 TATA-TTTCTATATATTTTTTA
*
48130632 TAAAATTT-TATA-ATTTTTTA
1 T-ATATTTCTATATATTTTTTA
48130652 TATATTTCTATATATTTT
1 TATATTTCTATATATTTT
48130670 ATTTTTTACG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
19 12 0.27
20 19 0.43
21 13 0.30
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATTTCTATATATTTTTTA
Found at i:48135280 original size:27 final size:25
Alignment explanation
Indices: 48135232--48135281 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
48135222 TTTGACTCTA
*
48135232 ATTTTTTTTAAATTTCTCTCAATTT
1 ATTTTTTTTAAATTTATCTCAATTT
*
48135257 ATTTATTTTTAACTTTATCGTCAAT
1 ATTT-TTTTTAAATTTATC-TCAAT
48135282 ATGCTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTTTTTTTAAATTTATCTCAATTT
Found at i:48135376 original size:11 final size:11
Alignment explanation
Indices: 48135356--48135399 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
48135346 CTCAACACCA
48135356 AAATTGAGAGG
1 AAATTGAGAGG
*
48135367 AAATTTAGAGG
1 AAATTGAGAGG
*
48135378 AAACTGAGAGG
1 AAATTGAGAGG
48135389 AAATTTGAGAG
1 AAA-TTGAGAG
48135400 ATGATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.20
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:48137609 original size:3 final size:3
Alignment explanation
Indices: 48137601--48137625 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48137591 TAACAATCAA
48137601 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
48137626 GCATCTTCCT
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:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:48142480 original size:2 final size:2
Alignment explanation
Indices: 48142473--48142522 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
48142463 GTATTCCTAA
48142473 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
48142515 AT AT AT AT
1 AT AT AT AT
48142523 CTAATACATA
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:48143494 original size:21 final size:20
Alignment explanation
Indices: 48143469--48143520 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
48143459 GGTTATTCAT
*
48143469 TTTTTTATAATTTTGTATGTA
1 TTTTTTATAAATTT-TATGTA
*
48143490 -TTTTTATAAAATTTTATGTG
1 TTTTTTAT-AAATTTTATGTA
48143510 TTTTTTATAAA
1 TTTTTTATAAA
48143521 AAACGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTTTATAAATTTTATGTA
Found at i:48143502 original size:22 final size:22
Alignment explanation
Indices: 48143467--48143521 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
48143457 ATGGTTATTC
* * *
48143467 ATTTTTTTATAATTTTGTATGT
1 ATTTTTATAAAATTTTATATGT
*
48143489 ATTTTTATAAAATTTTATGTGT
1 ATTTTTATAAAATTTTATATGT
48143511 -TTTTTATAAAA
1 ATTTTTATAAAA
48143522 AACGAACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTTTATAAAATTTTATATGT
Found at i:48143521 original size:21 final size:21
Alignment explanation
Indices: 48143468--48143521 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
48143458 TGGTTATTCA
*
48143468 TTTTTTTAT-AATTTTGTATG
1 TTTTTTTATAAAATTTGTATG
*
48143488 TATTTTTATAAAATTT-TATG
1 TTTTTTTATAAAATTTGTATG
48143508 TGTTTTTTATAAAA
1 T-TTTTTTATAAAA
48143522 AACGAACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTTTTATAAAATTTGTATG
Found at i:48143573 original size:10 final size:10
Alignment explanation
Indices: 48143558--48143591 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
48143548 GAAAGTTTTT
48143558 ATTTTTTAAA
1 ATTTTTTAAA
48143568 ATTTTTT-AA
1 ATTTTTTAAA
48143577 A-TTTTTAAA
1 ATTTTTTAAA
48143586 ATTTTT
1 ATTTTT
48143592 AAGAATCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 6 0.27
10 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:48143592 original size:9 final size:9
Alignment explanation
Indices: 48143560--48143593 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
48143550 AAGTTTTTAT
48143560 TTTTTAAAA
1 TTTTTAAAA
*
48143569 TTTTTTAAA
1 TTTTTAAAA
48143578 TTTTTAAAA
1 TTTTTAAAA
48143587 TTTTTAA
1 TTTTTAA
48143594 GAATCAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:48144700 original size:5 final size:5
Alignment explanation
Indices: 48144690--48144716 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
48144680 TTGCATTTTA
48144690 CATAC CATAC CATAC CATAC CATAC CA
1 CATAC CATAC CATAC CATAC CATAC CA
48144717 CTTTACAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (5 bp):
CATAC
Found at i:48149512 original size:21 final size:18
Alignment explanation
Indices: 48149481--48149539 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
48149471 AATTTATTGT
48149481 AATATTATTTAAATTTTTA
1 AATATTATTT-AATTTTTA
48149500 AATATCTATTTTAA-TTTT-
1 AATAT-TA-TTTAATTTTTA
*
48149518 AATAGTGTATTTAATTTATA
1 AATA-T-TATTTAATTTTTA
48149538 AA
1 AA
48149540 AGTATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 6 0.18
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
AATATTATTTAATTTTTA
Found at i:48153183 original size:3 final size:3
Alignment explanation
Indices: 48153175--48153200 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48153165 ACGTTAACAT
48153175 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
48153201 TATATGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:48158298 original size:4 final size:5
Alignment explanation
Indices: 48158273--48158301 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
48158263 CCTAATTCAA
48158273 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
48158302 TTAATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:48164502 original size:2 final size:2
Alignment explanation
Indices: 48164495--48164521 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48164485 GTACAGTGTA
48164495 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
48164522 AAAGGAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48182700 original size:39 final size:39
Alignment explanation
Indices: 48182646--48182722 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
48182636 GATTTAAGAC
48182646 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTATA
1 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTATA
48182685 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTAT
1 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTAT
48182723 GTATAGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (39 bp):
TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTATA
Found at i:48188668 original size:25 final size:25
Alignment explanation
Indices: 48188635--48188704 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
48188625 TTAAAATTTG
* * **
48188635 AAAAGTAAAAGAACTAAAAATGACC
1 AAAATTAAAGGAACTAAAAATGAAA
48188660 AAAATTAAAGGAACTAAAAATGAAA
1 AAAATTAAAGGAACTAAAAATGAAA
48188685 AAAATTAAAGGAACTAAAAA
1 AAAATTAAAGGAACTAAAAA
48188705 AAATTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.14
Consensus pattern (25 bp):
AAAATTAAAGGAACTAAAAATGAAA
Found at i:48195580 original size:17 final size:17
Alignment explanation
Indices: 48195553--48195598 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
48195543 CCGATATAAT
* * *
48195553 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
48195570 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
48195587 AAATATTTTTAA
1 AAATATTTTTAA
48195599 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:48195613 original size:12 final size:11
Alignment explanation
Indices: 48195582--48195623 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
48195572 ATTTTTTTAA
48195582 TTTTAAAATAT
1 TTTTAAAATAT
48195593 TTTTAAAATACT
1 TTTTAAAATA-T
*
48195605 TTTT-TAA-AT
1 TTTTAAAATAT
48195614 TTTTAAAATA
1 TTTTAAAATA
48195624 AATTTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 13 0.50
12 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:48195629 original size:21 final size:21
Alignment explanation
Indices: 48195591--48195630 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48195581 ATTTTAAAAT
**
48195591 ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
48195612 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
48195631 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:48195637 original size:22 final size:22
Alignment explanation
Indices: 48195589--48195648 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
48195579 TAATTTTAAA
* *
48195589 ATATTTTTAAAAT-ACTTTTTT
1 ATATTTTTAAAATAAATTTTTG
*
48195610 AAATTTTTAAAATAAATTTTTG
1 ATATTTTTAAAATAAATTTTTG
*
48195632 GTATTTATTAAAA-AAAT
1 ATATTT-TTAAAATAAAT
48195649 GGGCCGGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 12 0.38
22 14 0.44
23 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (22 bp):
ATATTTTTAAAATAAATTTTTG
Found at i:48213570 original size:37 final size:35
Alignment explanation
Indices: 48213520--48213628 Score: 89
Period size: 37 Copynumber: 3.0 Consensus size: 35
48213510 TATTCCAAAA
*
48213520 AATATTATTTTAATAGT-TTAATATTAAATTTAATGT
1 AATATTATCTTAATAGTATT-ATATT-AATTTAATGT
* *
48213556 AATACTTATCTTAATAGTATTTTATTAATTTAATTTT
1 AATA-TTATCTTAATAGTATTATATTAATTTAA-TGT
* *
48213593 AAAGTGATTATCTTAATATTA-AAT-TTAATTTAATGT
1 -AA-T-ATTATCTTAATAGTATTATATTAATTTAATGT
48213629 TTACCTTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
36 13 0.22
37 27 0.45
38 5 0.08
39 14 0.23
40 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (35 bp):
AATATTATCTTAATAGTATTATATTAATTTAATGT
Found at i:48213594 original size:25 final size:27
Alignment explanation
Indices: 48213566--48213621 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
48213556 AATACTTATC
* *
48213566 TTAATAGT-ATTTTATTAAT-TTAATT
1 TTAATAGTGATTATATTAATATTAAAT
*
48213591 TTAA-AGTGATTATCTTAATATTAAAT
1 TTAATAGTGATTATATTAATATTAAAT
48213617 TTAAT
1 TTAAT
48213622 TTAATGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
TTAATAGTGATTATATTAATATTAAAT
Found at i:48218597 original size:13 final size:13
Alignment explanation
Indices: 48218563--48218611 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
48218553 GACATGGGCG
*
48218563 TGTGACTCAGCCA
1 TGTGACACAGCCA
*
48218576 TGTGAGACACAGCCT
1 TGT--GACACAGCCA
*
48218591 TGTGACACGGCCA
1 TGTGACACAGCCA
48218604 TGTGACAC
1 TGTGACAC
48218612 CTGATGGTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 19 0.63
15 11 0.37
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (13 bp):
TGTGACACAGCCA
Found at i:48218678 original size:25 final size:25
Alignment explanation
Indices: 48218644--48218701 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
48218634 TCAATGAGTT
* *
48218644 ACACGGCCTGGCACACAGGTGTGTG
1 ACACGGCCTGGCACACAAGCGTGTG
*
48218669 ACACGGCCTGGCACATAAGCGTGTG
1 ACACGGCCTGGCACACAAGCGTGTG
48218694 ACACGGCC
1 ACACGGCC
48218702 GTGTGACCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.14
Consensus pattern (25 bp):
ACACGGCCTGGCACACAAGCGTGTG
Found at i:48224539 original size:16 final size:17
Alignment explanation
Indices: 48224517--48224556 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
48224507 TCACTATTAG
*
48224517 ATTTTATTATA-TTTAT
1 ATTTTATCATATTTTAT
*
48224533 GTTTTATCATATTTTAT
1 ATTTTATCATATTTTAT
48224550 ATTTTAT
1 ATTTTAT
48224557 AATTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTATCATATTTTAT
Found at i:48226227 original size:49 final size:49
Alignment explanation
Indices: 48226107--48226229 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
48226097 ATGGTATTAA
* * * *
48226107 ACTTGAACCCGTGACTATATAATCACCGTCAACTAGGGACCCGAGTTAT
1 ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGACCCGAGTTAT
* * *
48226156 ACTTCAACCTATGACTGCATAACCACCGTCAACTA-GGAGCCCTAGTTAT
1 ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGA-CCCGAGTTAT
48226205 ACTTCAACCCATGA-TCGTATAACCA
1 ACTTCAACCCATGACT-GTATAACCA
48226230 TTGTGAACTG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 4 0.06
49 59 0.94
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (49 bp):
ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGACCCGAGTTAT
Found at i:48229135 original size:50 final size:50
Alignment explanation
Indices: 48229028--48229274 Score: 219
Period size: 50 Copynumber: 4.8 Consensus size: 50
48229018 ATTTGGGTAA
* * *
48229028 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGACTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
48229084 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
48229134 AGAGGTCCCCCGTAAGACCATGTCTGGGAAATGGTATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
48229184 AGAATTCCCATGTAAGACCATATTTGGGATATGGCATTGGCA--GTATAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
48229233 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
48229275 TGTTATTATC
Statistics
Matches: 160, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
49 39 0.24
50 78 0.49
53 3 0.02
55 1 0.01
56 39 0.24
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:48231741 original size:19 final size:18
Alignment explanation
Indices: 48231719--48231763 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
48231709 ATTTTTTAAG
**
48231719 TTCATTTTTATTTTTATTT
1 TTCATTTTTATTTGCA-TT
*
48231738 TTCATTTATATTTGCATT
1 TTCATTTTTATTTGCATT
48231756 TTCATTTT
1 TTCATTTT
48231764 GGAGAAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (18 bp):
TTCATTTTTATTTGCATT
Found at i:48232567 original size:17 final size:18
Alignment explanation
Indices: 48232545--48232597 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
48232535 ACTTAATCAC
*
48232545 TTTAATATTAA-ATTTAA
1 TTTAATATTAATATTAAA
*
48232562 TTTAATATAAATATTAAA
1 TTTAATATTAATATTAAA
*
48232580 TTAAAT-TTAATATTAAA
1 TTTAATATTAATATTAAA
48232597 T
1 T
48232598 CTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 21 0.68
18 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATATTAATATTAAA
Found at i:48232577 original size:23 final size:24
Alignment explanation
Indices: 48232530--48232597 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 24
48232520 TTCAACTATG
* *
48232530 ATTAAACTTAATCACTTTAATATTAA
1 ATTAAATTTAAT-A-TTAAATATTAA
*
48232556 ATTTAATTTAATA-TAAATATTAA
1 ATTAAATTTAATATTAAATATTAA
48232579 ATTAAATTTAATATTAAAT
1 ATTAAATTTAATATTAAAT
48232598 CTTATTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 21 0.57
24 5 0.14
25 1 0.03
26 10 0.27
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTAAATTTAATATTAAATATTAA
Found at i:48232608 original size:23 final size:22
Alignment explanation
Indices: 48232548--48232606 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
48232538 TAATCACTTT
*
48232548 AATATTAAATTTAATTTAATATA
1 AATATT-AATTAAATTTAATATA
48232571 AATATTAAATTAAATTTAATATTA
1 AATATT-AATTAAATTTAATA-TA
*
48232595 AATCTT-ATTAAA
1 AATATTAATTAAA
48232607 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 6 0.18
23 20 0.61
24 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATTAATTAAATTTAATATA
Found at i:48232641 original size:62 final size:62
Alignment explanation
Indices: 48232568--48232719 Score: 268
Period size: 62 Copynumber: 2.5 Consensus size: 62
48232558 TTAATTTAAT
* *
48232568 ATAAATATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAAAATGTTTATCTACAAG
1 ATAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAAAATATTTATCTACAAG
* *
48232630 ATAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAGATTATTTATCTACAAG
1 ATAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAAAATATTTATCTACAAG
48232692 ATAAACATTAAATTAAATTTAATATTAA
1 ATAAACATTAAATTAAATTTAATATTAA
48232720 GATAATCACT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 86 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (62 bp):
ATAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAAAATATTTATCTACAAG
Found at i:48232745 original size:20 final size:18
Alignment explanation
Indices: 48232698--48232746 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
48232688 CAAGATAAAC
48232698 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
48232715 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
48232735 ATTAAATTAATA
1 ATTAAATTAATA
48232747 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:48233137 original size:20 final size:20
Alignment explanation
Indices: 48233121--48233157 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
48233111 TTGATTTTGG
48233121 GATCCCAGGCCCAA-TTTAC
1 GATCCCAGGCCCAATTTTAC
*
48233140 GATCCCAGGTCCAATTTT
1 GATCCCAGGCCCAATTTT
48233158 CAAGTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 13 0.81
20 3 0.19
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.27
Consensus pattern (20 bp):
GATCCCAGGCCCAATTTTAC
Found at i:48233243 original size:9 final size:9
Alignment explanation
Indices: 48233219--48233258 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
48233209 AAAATATCAT
48233219 ATTAATTTTA
1 ATTAA-TTTA
*
48233229 ATTAATTTG
1 ATTAATTTA
48233238 ATTAATTTA
1 ATTAATTTA
48233247 ATTAATTTA
1 ATTAATTTA
48233256 ATT
1 ATT
48233259 TTACTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 23 0.82
10 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:48239796 original size:32 final size:32
Alignment explanation
Indices: 48239754--48239814 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
48239744 TCAACTCAAA
48239754 TATATCATGTTATAA-AAAAATTATTATATTAAT
1 TATATCATGTTA-AATAAAAATTA-TATATTAAT
*
48239787 TATAT-ATGTTAAATAATAATTATATATT
1 TATATCATGTTAAATAAAAATTATATATT
48239815 TTTATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 8 0.31
32 13 0.50
33 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (32 bp):
TATATCATGTTAAATAAAAATTATATATTAAT
Found at i:48243647 original size:8 final size:8
Alignment explanation
Indices: 48243631--48243661 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
48243621 TTAGGTTAAA
*
48243631 TTATATTT
1 TTATTTTT
48243639 TTATTTTT
1 TTATTTTT
48243647 TTATTTTT
1 TTATTTTT
48243655 TTATTTT
1 TTATTTT
48243662 GAGCAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTATTTTT
Found at i:48244556 original size:2 final size:2
Alignment explanation
Indices: 48244549--48244573 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48244539 TAAATTCATT
48244549 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
48244574 TGTTGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48257572 original size:48 final size:48
Alignment explanation
Indices: 48257506--48257613 Score: 189
Period size: 48 Copynumber: 2.2 Consensus size: 48
48257496 CTATTTAATC
* *
48257506 ATCAATTAAATCATTTTTTTTATAATTTTTAATAATTTATTCAATCAA
1 ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTCAATCAA
*
48257554 ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTGAATCAA
1 ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTCAATCAA
48257602 ATCAATTAAATT
1 ATCAATTAAATT
48257614 GATGGCTTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (48 bp):
ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTCAATCAA
Found at i:48262654 original size:4 final size:4
Alignment explanation
Indices: 48262647--48262736 Score: 180
Period size: 4 Copynumber: 22.5 Consensus size: 4
48262637 ACACACACAT
48262647 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
48262695 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
48262737 GATTTGTTAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 86 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:48265121 original size:4 final size:4
Alignment explanation
Indices: 48265112--48265359 Score: 397
Period size: 4 Copynumber: 62.0 Consensus size: 4
48265102 GAAAATAAAC
48265112 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
48265160 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GGAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * *
48265208 GTAT GCAT GTAT GCAT GTAT GCAT GTAT GCAT GCAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
48265256 GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
48265304 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTTT GTTT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
48265352 GTAT GTAT
1 GTAT GTAT
48265360 TCATTTATTT
Statistics
Matches: 227, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 227 1.00
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:48270349 original size:10 final size:10
Alignment explanation
Indices: 48270336--48270398 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
48270326 TTTAAAATAT
48270336 TTTTTTTAAA
1 TTTTTTTAAA
*
48270346 TTTTTTTTAA
1 TTTTTTTAAA
48270356 ---TTTTAAA
1 TTTTTTTAAA
48270363 TTTTTTTAAAA
1 TTTTTTT-AAA
*
48270374 TACTTTTTTTAA
1 T--TTTTTTAAA
48270386 TTTTTTT-AA
1 TTTTTTTAAA
48270395 TTTT
1 TTTT
48270399 AAAATAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
7 6 0.14
9 6 0.14
10 19 0.43
11 4 0.09
12 3 0.07
13 6 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:48270350 original size:40 final size:39
Alignment explanation
Indices: 48270305--48270430 Score: 155
Period size: 40 Copynumber: 3.2 Consensus size: 39
48270295 AAATATTTTT
* *
48270305 ATTTTTTAACTTTAAAATACTTTTAAAATATTTTTTTTAA
1 ATTTTTTAA-TTTAAAATAATTTTAAAATACTTTTTTTAA
* **
48270345 ATTTTTTTTAATTTTAAATTTTTTTAAAATACTTTTTTTAA
1 A--TTTTTTAATTTAAAATAATTTTAAAATACTTTTTTTAA
*
48270386 TTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTT-A
1 ATTTTTTAA-TTTAAAATAATTTTAAAATACTTTTTTTAA
48270425 ATTTTT
1 ATTTTT
48270431 ATTTTAATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.19
40 26 0.35
41 26 0.35
42 8 0.11
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (39 bp):
ATTTTTTAATTTAAAATAATTTTAAAATACTTTTTTTAA
Found at i:48270381 original size:30 final size:28
Alignment explanation
Indices: 48270334--48270389 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
48270324 CTTTTAAAAT
*
48270334 ATTTTTTTTAAATTTTTTTTAATTTTAA
1 ATTTTTTTAAAATTTTTTTTAATTTTAA
48270362 ATTTTTTTAAAATACTTTTTTTAATTTT
1 ATTTTTTTAAAAT--TTTTTTTAATTTT
48270390 TTTAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
30 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (28 bp):
ATTTTTTTAAAATTTTTTTTAATTTTAA
Found at i:48270439 original size:32 final size:32
Alignment explanation
Indices: 48270386--48270448 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
48270376 CTTTTTTTAA
48270386 TTTTTTTAATTTTAAAATAA-TTTTAAAATAC
1 TTTTTTTAATTTTAAAATAATTTTTAAAATAC
***
48270417 TTTTTTTAATTTTTATTTTAATTTTTAAAATA
1 TTTTTTTAA-TTTTAAAATAATTTTTAAAATA
48270449 AATTTTTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 9 0.33
32 8 0.30
33 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTTTTTAATTTTAAAATAATTTTTAAAATAC
Found at i:48274172 original size:14 final size:14
Alignment explanation
Indices: 48274153--48274192 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
48274143 TTGATTGCCA
48274153 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
48274167 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
48274181 GGAAAATGTTTT
1 GTAAAATGTTTT
48274193 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:48274201 original size:20 final size:20
Alignment explanation
Indices: 48274176--48274216 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
48274166 CGTAAAATGA
*
48274176 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
48274196 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
48274216 T
1 T
48274217 GAAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:48274205 original size:34 final size:35
Alignment explanation
Indices: 48274161--48274227 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
48274151 CAGTAAAATG
*
48274161 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
48274195 TTTTCTGTAAAATGATTTACTTGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
48274228 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:48277749 original size:2 final size:2
Alignment explanation
Indices: 48277742--48277799 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
48277732 GCCGGTAAAT
* * * * * *
48277742 TC TC TC TC TC TC TC CC CC CC TC TC CC TC TC CC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
48277784 CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
48277800 ATTTTTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (2 bp):
TC
Found at i:48277770 original size:16 final size:18
Alignment explanation
Indices: 48277743--48277799 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
48277733 CCGGTAAATT
*
48277743 CTCTCTCTCTCTCCC-CC
1 CTCTCTCCCTCTCCCTCC
48277760 C-CTCTCCCTCTCCCTCC
1 CTCTCTCCCTCTCCCTCC
* *
48277777 CTCTCTCCCTCTCTCTCT
1 CTCTCTCCCTCTCCCTCC
48277795 CTCTC
1 CTCTC
48277800 ATTTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.34
17 4 0.11
18 19 0.54
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (18 bp):
CTCTCTCCCTCTCCCTCC
Found at i:48280832 original size:50 final size:50
Alignment explanation
Indices: 48280757--48280855 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
48280747 TGAATTTTTA
*
48280757 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTGAATAATTAGATATT
1 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
48280807 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATAT
1 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATAT
48280856 CATAGTTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (50 bp):
TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
Found at i:48285615 original size:2 final size:2
Alignment explanation
Indices: 48285608--48285642 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48285598 TAAAATATGC
48285608 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
48285643 TTGTAGTTTT
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:48285936 original size:20 final size:19
Alignment explanation
Indices: 48285889--48285936 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
48285879 TAAACCGCAG
* *
48285889 TTAAACTCACCCTAAGTTT
1 TTAATCTCACCCTAAGTAT
* *
48285908 TTTATCTCACGCTATAGTAT
1 TTAATCTCACCCTA-AGTAT
48285928 TTAATCTCA
1 TTAATCTCA
48285937 ACGCCACTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (19 bp):
TTAATCTCACCCTAAGTAT
Found at i:48285962 original size:78 final size:78
Alignment explanation
Indices: 48285828--48285983 Score: 240
Period size: 78 Copynumber: 2.0 Consensus size: 78
48285818 TTTAGCTTAC
* * *
48285828 TTTTTGTCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTTACATAAACCGCAGTTAA
1 TTTTTATCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTAACACAAACCGCAGTTAA
48285893 ACTCACCCTAAGT
66 ACTCACCCTAAGT
* * * * *
48285906 TTTTTATCTCACGCTATAGTATTTAATCTCAACGCCACTACTGTTTTAACACAAACCGCAGTTAA
1 TTTTTATCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTAACACAAACCGCAGTTAA
48285971 ACTCACCCTAAGT
66 ACTCACCCTAAGT
48285984 GAGTTTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.33
Consensus pattern (78 bp):
TTTTTATCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTAACACAAACCGCAGTTAA
ACTCACCCTAAGT
Found at i:48297155 original size:25 final size:24
Alignment explanation
Indices: 48297109--48297155 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
48297099 TATATTTCAT
*
48297109 ATATCATTATATTAAATTATTTAA
1 ATATCATTATATTAAATGATTTAA
* *
48297133 ATATCATATATCTTAACTGATTT
1 ATATCAT-TATATTAAATGATTT
48297156 TTTACTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATCATTATATTAAATGATTTAA
Found at i:48299714 original size:44 final size:44
Alignment explanation
Indices: 48299651--48299813 Score: 229
Period size: 44 Copynumber: 3.6 Consensus size: 44
48299641 TTTGAGTACT
* *
48299651 TCTGATCAGTGACAAGTGATTAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
48299695 TCTGATTAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
48299739 TCTGATCAATGACAAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGATC-A-G----G-GACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
48299789 TCTGATCAGGGACAAGTGATAAGTG
1 TCTGATCAGGGACAAGTGATAAGTG
48299814 ATCATACGTA
Statistics
Matches: 108, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
43 15 0.14
44 48 0.44
45 1 0.01
46 1 0.01
48 1 0.01
49 1 0.01
50 21 0.19
51 20 0.19
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Done.