Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 191 of 205
Found at i:56702055 original size:16 final size:16
Alignment explanation
Indices: 56702014--56702055 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
56702004 CCCCCAACTT
* *
56702014 CCCCGATTTCATTTTC
1 CCCCAATTTCCTTTTC
56702030 CCCCAA-TTCCTTTTC
1 CCCCAATTTCCTTTTC
56702045 CCCCAATTTCC
1 CCCCAATTTCC
56702056 CCGATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.14, C:0.45, G:0.02, T:0.38
Consensus pattern (16 bp):
CCCCAATTTCCTTTTC
Found at i:56703941 original size:60 final size:60
Alignment explanation
Indices: 56703868--56703986 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
56703858 ATTGTTGTAA
*
56703868 TTAGTTATTAAGTTTTC-AACTATTTTATGTGTATTGCAGATAAAATGCCTAGAAGAAAAT
1 TTAGTTATTAAGTTTACTAAC-ATTTTATGTGTATTGCAGATAAAATGCCTAGAAGAAAAT
*
56703928 TTAGTTATTAAGTTTACTTACATTTTATGTGTATTGCAGATAAAATGCCTAGAAGAAAA
1 TTAGTTATTAAGTTTACTAACATTTTATGTGTATTGCAGATAAAATGCCTAGAAGAAAA
56703987 ATTCTAAGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (60 bp):
TTAGTTATTAAGTTTACTAACATTTTATGTGTATTGCAGATAAAATGCCTAGAAGAAAAT
Found at i:56705554 original size:21 final size:21
Alignment explanation
Indices: 56705528--56705596 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
56705518 CAACAACTTA
* *
56705528 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
**
56705549 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
56705570 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
56705591 AAGCAG
1 AAGCAG
56705597 CGAGAGAAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.43, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:56705598 original size:12 final size:12
Alignment explanation
Indices: 56705561--56705608 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
56705551 GCAGAGGCTA
56705561 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
56705573 CA--GAG-GCCG
1 CAGCGAGAGAAG
56705582 CAGCGAGAGAAG
1 CAGCGAGAGAAG
56705594 CAGCGAGAGAAG
1 CAGCGAGAGAAG
56705606 CAG
1 CAG
56705609 AGGTTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 4 0.14
10 3 0.10
11 3 0.10
12 19 0.66
ACGTcount: A:0.38, C:0.21, G:0.42, T:0.00
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:56706032 original size:43 final size:43
Alignment explanation
Indices: 56705984--56706084 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
56705974 ATCCCAAAAT
*
56705984 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAA-AGTCA-TATCATA
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCGAAAGAG-CACTA-CATA
* * * * *
56706027 TAGTGGCGTTTGTGAAATAAGCGCCGCGAAAGAGCACTACTTT
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCGAAAGAGCACTACATA
56706070 TAGTGGCGTTTTTTA
1 TAGTGGCGTTTTTTA
56706085 CCAAGTGCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 44 0.92
44 4 0.08
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
TAGTGGCGTTTTTTAAAAAAGCGCCGCGAAAGAGCACTACATA
Found at i:56706137 original size:42 final size:42
Alignment explanation
Indices: 56706044--56706272 Score: 183
Period size: 43 Copynumber: 5.4 Consensus size: 42
56706034 GTTTGTGAAA
* * * * *
56706044 TAAGCGCCGCGAAAGAGCACTACTTTTAGTGGCGTTTTTTAC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
* * *
56706086 CAAGTGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
* * * * * * * *
56706128 TAAACGCCGCTAAAGATCATGT-TTCTTTAACTGTGTTTTCTCC
1 TAAGCGCCGCTAAAGAACAT-TACT-TTTAGCGGCGTTTTTTTC
* * * *
56706171 CAAGCGCCGCTAAAGAACATGA-TCATTAGCAGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTTC
* *
56706213 TTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTC
1 -TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
*
56706256 TGTAAGCGCCGCAAAAG
1 --TAAGCGCCGCTAAAG
56706273 TTAGCGACAT
Statistics
Matches: 146, Mismatches: 35, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
42 64 0.44
43 68 0.47
44 14 0.10
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
Found at i:56706166 original size:85 final size:86
Alignment explanation
Indices: 56706077--56706234 Score: 212
Period size: 85 Copynumber: 1.8 Consensus size: 86
56706067 TTTTAGTGGC
* * * * * *
56706077 GTTTTTTACCAAGTGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTTTTC-TAAACGCCGCTA
1 GTTTTCTACCAAGCGCCGCTAAAGAACATGATC-ATTAGCAGCGTTTTTTTCTTAAACGCCGCTA
*
56706140 AAGATCATGTTTCTTTAACTGT
65 AAGAACATGTTTCTTTAACTGT
* *
56706162 GTTTTCTCCCAAGCGCCGCTAAAGAACATGATCATTAGCAGCGTTTTTTTCTTAAGCGCCGCTAA
1 GTTTTCTACCAAGCGCCGCTAAAGAACATGATCATTAGCAGCGTTTTTTTCTTAAACGCCGCTAA
56706227 AGAACATG
66 AGAACATG
56706235 ACCTTTAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 42 0.68
86 20 0.32
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (86 bp):
GTTTTCTACCAAGCGCCGCTAAAGAACATGATCATTAGCAGCGTTTTTTTCTTAAACGCCGCTAA
AGAACATGTTTCTTTAACTGT
Found at i:56706251 original size:85 final size:84
Alignment explanation
Indices: 56706044--56706251 Score: 204
Period size: 85 Copynumber: 2.5 Consensus size: 84
56706034 GTTTGTGAAA
* * * * * * * *
56706044 TAAGCGCCGCGAAAGAGCACT-ACTTTTAGTGGCGTTTTTTACCAAGTGCCGCTATAGAACATTA
1 TAAGCGCCGCTAAAGAACA-TGACCTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGA
* *
56706108 CTTTTAGCGGCGTTTTTTTC
65 CTATTAGCAGCGTTTTTTTC
* * ** * * * *
56706128 TAAACGCCGCTAAAGATCATGTTTCTTTAACTGTGTTTTCTCCCAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATG-ACCTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGA
56706193 -TCATTAGCAGCGTTTTTTTC
65 CT-ATTAGCAGCGTTTTTTTC
56706213 TTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT
1 -TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT
56706252 TTTCTGTAAG
Statistics
Matches: 96, Mismatches: 24, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
83 1 0.01
84 17 0.18
85 59 0.61
86 19 0.20
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGAC
TATTAGCAGCGTTTTTTTC
Found at i:56706790 original size:24 final size:25
Alignment explanation
Indices: 56706752--56706803 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
56706742 ACACGTTAGC
56706752 AAACAAAAATATATAAATAT-AAAT
1 AAACAAAAATATATAAATATAAAAT
* * *
56706776 AAACAAATATTTATATATATAAAAT
1 AAACAAAAATATATAAATATAAAAT
56706801 AAA
1 AAA
56706804 TTGAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAACAAAAATATATAAATATAAAAT
Found at i:56710418 original size:42 final size:42
Alignment explanation
Indices: 56710372--56710455 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
56710362 CAAATTGACG
56710372 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
*
56710414 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAGAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
56710456 AATTCCGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (42 bp):
GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
Found at i:56712584 original size:4 final size:4
Alignment explanation
Indices: 56712575--56712608 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
56712565 AAGTTTTATT
56712575 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
56712609 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:56712616 original size:22 final size:22
Alignment explanation
Indices: 56712558--56712617 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
56712548 AAGTGGCCCA
*
56712558 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
56712582 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
56712603 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
56712618 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:56720080 original size:6 final size:6
Alignment explanation
Indices: 56720069--56720103 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
56720059 GTAATTAGTG
56720069 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
56720104 CACACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:56720110 original size:18 final size:18
Alignment explanation
Indices: 56720071--56720111 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
56720061 AATTAGTGAT
* *
56720071 ACATATACATATACATAT
1 ACATATACATATACACAC
56720089 ACATATACATATACACAC
1 ACATATACATATACACAC
56720107 ACATA
1 ACATA
56720112 CAAATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (18 bp):
ACATATACATATACACAC
Found at i:56720198 original size:16 final size:16
Alignment explanation
Indices: 56720179--56720213 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56720169 TAGATAAATA
*
56720179 CATACATACAGACATG
1 CATACATAAAGACATG
*
56720195 CATACATAAATACATG
1 CATACATAAAGACATG
56720211 CAT
1 CAT
56720214 GCATGCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (16 bp):
CATACATAAAGACATG
Found at i:56732815 original size:18 final size:18
Alignment explanation
Indices: 56732788--56732880 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
56732778 TACGACCGTT
56732788 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
56732806 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
56732824 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
56732842 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
56732860 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
56732878 TAC
1 TAC
56732881 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:56743211 original size:22 final size:21
Alignment explanation
Indices: 56743180--56743221 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
56743170 TTATTTAATT
*
56743180 TAAATTTTTTATGATGTAAAAA
1 TAAATATTTTAT-ATGTAAAAA
*
56743202 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATGTAAAA
56743222 TACTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAATATTTTATATGTAAAAA
Found at i:56749135 original size:48 final size:48
Alignment explanation
Indices: 56749067--56749226 Score: 250
Period size: 48 Copynumber: 3.3 Consensus size: 48
56749057 AAGGTATATT
* * *
56749067 TGTCTTTCACTATTTGCACTCTTAGAGTTGGTAC-TTTATTGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTA-TGTATGGCA
*
56749115 TGTCATTCATTATTTTCACTCTTAGAGTTGGTGCTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
* *
56749163 TGTCATTCATTATTTTCACTCTTAGATTTTGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
56749211 TGTCATTCATTATTTT
1 TGTCATTCATTATTTT
56749227 TATTGATAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 100 0.96
49 4 0.04
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (48 bp):
TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
Found at i:56754201 original size:3 final size:3
Alignment explanation
Indices: 56754193--56754246 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
56754183 AATACACCAA
56754193 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56754241 AAT AAT
1 AAT AAT
56754247 GGTAAGAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56766691 original size:13 final size:13
Alignment explanation
Indices: 56766675--56766720 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
56766665 CTTTGCTTTT
56766675 GAAAAGTGCTGTG
1 GAAAAGTGCTGTG
* *
56766688 GAAAAGTGCTTTT
1 GAAAAGTGCTGTG
* *
56766701 GAGAAGTGTTGTG
1 GAAAAGTGCTGTG
56766714 GAAAAGT
1 GAAAAGT
56766721 TTGGTTTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (13 bp):
GAAAAGTGCTGTG
Found at i:56766697 original size:26 final size:26
Alignment explanation
Indices: 56766668--56766720 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
56766658 AGTTCTTCTT
56766668 TGCTTTTGAAAAGTGCTGTGGAAAAG
1 TGCTTTTGAAAAGTGCTGTGGAAAAG
* *
56766694 TGCTTTTGAGAAGTGTTGTGGAAAAG
1 TGCTTTTGAAAAGTGCTGTGGAAAAG
56766720 T
1 T
56766721 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.34
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTGTGGAAAAG
Found at i:56769767 original size:16 final size:18
Alignment explanation
Indices: 56769729--56769766 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
56769719 TTGATTCATA
*
56769729 TTTTATCCGAGTCTAATT
1 TTTTATCCAAGTCTAATT
56769747 TTTTATCCAAGTCT-ATT
1 TTTTATCCAAGTCTAATT
56769764 TTT
1 TTT
56769767 AGTACCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (18 bp):
TTTTATCCAAGTCTAATT
Found at i:56774942 original size:3 final size:3
Alignment explanation
Indices: 56774934--56774971 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
56774924 ACCGTGCATG
56774934 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56774972 ATTGTAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56775143 original size:34 final size:35
Alignment explanation
Indices: 56775105--56775189 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 35
56775095 TTATAAACAT
56775105 TAAAAAATTATTTTAAAA-ATAATAAAAAT-AAAAA
1 TAAAAAA-TATTTTAAAAGATAATAAAAATAAAAAA
**
56775139 T-AAAAATATTTTAAAAGTATTTTAAAAATAAAAAA
1 TAAAAAATATTTTAAAAG-ATAATAAAAATAAAAAA
56775174 TAAAAAAATATATTTA
1 T-AAAAAATAT-TTTA
56775190 TTATATTCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.23
33 5 0.12
34 10 0.23
35 6 0.14
37 8 0.19
38 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (35 bp):
TAAAAAATATTTTAAAAGATAATAAAAATAAAAAA
Found at i:56775153 original size:11 final size:11
Alignment explanation
Indices: 56775139--56775168 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
56775129 AAAATAAAAA
56775139 TAAAAATATTT
1 TAAAAATATTT
*
56775150 TAAAAGTATTT
1 TAAAAATATTT
56775161 TAAAAATA
1 TAAAAATA
56775169 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:56777508 original size:3 final size:3
Alignment explanation
Indices: 56777500--56777526 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
56777490 AACCCTTGAC
56777500 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
56777527 ATCCATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56778528 original size:126 final size:126
Alignment explanation
Indices: 56778284--56778586 Score: 318
Period size: 126 Copynumber: 2.4 Consensus size: 126
56778274 GTTAGAAGCT
* *
56778284 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTAATGGTGAAATGCTTGATGAAAA
1 CGCTATGAGAAGGATCAAAATACATCCAGAGATA--G-T-G--ATGGTGATATGCTCGATGAAAA
* * ** * * * * * *
56778349 TAGATCTACTGGCTCTCATAGTGAGGAGCAAGATCAGCACTTATTGGTAGAAGGGCGACGTAATG
60 TAGATCAACTGACTCTCATAGCAAGAAGCAAGATCAGAACTTATCGATAGAAGGCCAACGTAATG
*
56778414 GT
125 GA
* * *
56778416 TGCTATGAGAAGGAACAAAATGCATCCAGAGATAGTGATGGTGATATGCTCGATGAAAATAGATC
1 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGATATGCTCGATGAAAATAGATC
* * * * *
56778481 AACTGATTCTCGTAGCAAGAAGCACGGTGAGAACTTATCGATAGAAGGCCAACGTAATGGA
66 AACTGACTCTCATAGCAAGAAGCAAGATCAGAACTTATCGATAGAAGGCCAACGTAATGGA
* * * * *
56778542 CGCTACGAGAAAGATCAAGATACTTCCAGAGATGGTGATGGTGAT
1 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGAT
56778587 GGTGATGGTG
Statistics
Matches: 142, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
126 108 0.76
128 1 0.01
129 1 0.01
130 1 0.01
132 31 0.22
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (126 bp):
CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGATATGCTCGATGAAAATAGATC
AACTGACTCTCATAGCAAGAAGCAAGATCAGAACTTATCGATAGAAGGCCAACGTAATGGA
Found at i:56778581 original size:6 final size:6
Alignment explanation
Indices: 56778572--56778604 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
56778562 TACTTCCAGA
56778572 GATGGT GATGGT GATGGT GATGGT GATGGT GAT
1 GATGGT GATGGT GATGGT GATGGT GATGGT GAT
56778605 ATGGTTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.33
Consensus pattern (6 bp):
GATGGT
Found at i:56778737 original size:144 final size:143
Alignment explanation
Indices: 56778450--56778727 Score: 375
Period size: 144 Copynumber: 2.0 Consensus size: 143
56778440 TCCAGAGATA
*
56778450 GTGATGGTGATATGCTCGATGAAAATAGATCAACTGATTCTCGTAGCAAGAAGCACGGTGAGAAC
1 GTGATGGTGATATGCTCGATGAAAATAGATCAACTGATTCTCATAGCAAGAAGCACGGTGAGAAC
*
56778515 TTATCGATAGAAGGCCAACGTAATGGACGCTACGAGAAAGATCAAGATACTTCCAGAGATGGTGA
66 TTATCGATAGAAGGCCAAC-TAATGGACGCTACGAGAAAGATCAAGATACATCCAGAGATGGTGA
56778580 TGGTGATGGTGATG
130 TGGTGATGGTGATG
* * * * * * * *
56778594 GTGATGGTGATATGGTTGATGAAAGTAGGTCTATTGATTCTCATAGCGAGGAGCACGGTGAGAAC
1 GTGATGGTGATATGCTCGATGAAAATAGATCAACTGATTCTCATAGCAAGAAGCACGGTGAGAAC
* ** *
56778659 TTATCGGTAGAAGGCC-A-TAATGGTA-GCTACGAGGCAGATCAA-ATTGCATCCAGAGATGGTG
66 TTATCGATAGAAGGCCAACTAATGG-ACGCTACGAGAAAGATCAAGA-TACATCCAGAGATGGTG
56778720 ATGGTGAT
129 ATGGTGAT
56778728 ATGGTTGATG
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
140 1 0.01
141 44 0.37
142 1 0.01
143 1 0.01
144 71 0.60
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (143 bp):
GTGATGGTGATATGCTCGATGAAAATAGATCAACTGATTCTCATAGCAAGAAGCACGGTGAGAAC
TTATCGATAGAAGGCCAACTAATGGACGCTACGAGAAAGATCAAGATACATCCAGAGATGGTGAT
GGTGATGGTGATG
Found at i:56786856 original size:28 final size:28
Alignment explanation
Indices: 56786823--56786902 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
56786813 AGATTAATTG
* *
56786823 ACGAGTAGTGATCATTTTTATTACTAAT
1 ACGAGTAATGATCATTTTCATTACTAAT
* * * *
56786851 ATGAGTAATGATTATTTTCATTATTAGT
1 ACGAGTAATGATCATTTTCATTACTAAT
*
56786879 ACGAGTAAAGATCATTTTCATTAC
1 ACGAGTAATGATCATTTTCATTAC
56786903 AAAAGATACA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (28 bp):
ACGAGTAATGATCATTTTCATTACTAAT
Found at i:56788980 original size:18 final size:19
Alignment explanation
Indices: 56788937--56788978 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
56788927 GTACATTCGT
56788937 GTTTTGGTGTATGACGGGG
1 GTTTTGGTGTATGACGGGG
56788956 GTTTTGGTGTATGACGGGG
1 GTTTTGGTGTATGACGGGG
56788975 GTTT
1 GTTT
56788979 GGAGTGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.05, G:0.45, T:0.40
Consensus pattern (19 bp):
GTTTTGGTGTATGACGGGG
Found at i:56789118 original size:21 final size:21
Alignment explanation
Indices: 56789092--56789155 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
56789082 TTTTGGTGGA
*
56789092 TCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* **
56789113 TCAGCTCTCACAAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* *
56789134 TCATCTCGTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
56789155 T
1 T
56789156 AGCGTGTTCT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:56790636 original size:35 final size:34
Alignment explanation
Indices: 56790577--56790670 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 34
56790567 TGAATTGACG
* * * *
56790577 GATAAGACCATGGTTGGACCATGGCAATGTTTAAAT
1 GATAAGACCATAGCTGGGCTATGGCAAT-TTT-AAT
56790613 G-TAAGACCATAGCTGGGCTATGGC-ATTTTAAT
1 GATAAGACCATAGCTGGGCTATGGCAATTTTAAT
* * * *
56790645 GAAAATACCATAACTGGGTTATGGCA
1 GATAAGACCATAGCTGGGCTATGGCA
56790671 CAAAGAGACG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
32 4 0.08
33 22 0.46
34 2 0.04
35 19 0.40
36 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (34 bp):
GATAAGACCATAGCTGGGCTATGGCAATTTTAAT
Found at i:56791102 original size:37 final size:37
Alignment explanation
Indices: 56791052--56791153 Score: 107
Period size: 40 Copynumber: 2.7 Consensus size: 37
56791042 CGGATAAATT
* * *
56791052 CGATGAGGTACTGGGTATCAAATTACTTCGACA-TGGC
1 CGATGAGGCACTGGGTGTCAAATTACTTCGA-ATTAGC
* *
56791089 CGATGAGACACTGGGTGTCAATCTATTACTTCGAATTATC
1 CGATGAGGCACTGGGTGTCAA---ATTACTTCGAATTAGC
*
56791129 CGATGAGGCACTGGGTGCCAAATTA
1 CGATGAGGCACTGGGTGTCAAATTA
56791154 GTGTGTTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
37 22 0.41
39 1 0.02
40 31 0.57
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (37 bp):
CGATGAGGCACTGGGTGTCAAATTACTTCGAATTAGC
Found at i:56796219 original size:17 final size:17
Alignment explanation
Indices: 56796197--56796230 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56796187 AAATATAACA
*
56796197 TTTTTGAATAATACTTG
1 TTTTTGAATAAAACTTG
56796214 TTTTTGAATAAAACTTG
1 TTTTTGAATAAAACTTG
56796231 ATAAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTTTGAATAAAACTTG
Found at i:56798905 original size:53 final size:53
Alignment explanation
Indices: 56798810--56798916 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
56798800 GTTATAAATT
* * *
56798810 AATAAAGTTAATAATTAAAATTTGAAAAATTAAATTTTAGTAATCAAAATATA
1 AATAAAATTAATAATTAAAATTTGAAAAATTAAAATTGAGTAATCAAAATATA
56798863 AATAAAATTAATAATTAAAATATT-ACAAAA-TAAAATTGAGTAATCAAAATATA
1 AATAAAATTAATAATTAAAAT-TTGA-AAAATTAAAATTGAGTAATCAAAATATA
56798916 A
1 A
56798917 TTTAGTAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 43 0.88
54 6 0.12
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (53 bp):
AATAAAATTAATAATTAAAATTTGAAAAATTAAAATTGAGTAATCAAAATATA
Found at i:56798910 original size:19 final size:19
Alignment explanation
Indices: 56798888--56798925 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56798878 TAAAATATTA
56798888 CAAAATAAAATTGAGTAAT
1 CAAAATAAAATTGAGTAAT
* *
56798907 CAAAATATAATTTAGTAAT
1 CAAAATAAAATTGAGTAAT
56798926 ATTGTGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
CAAAATAAAATTGAGTAAT
Found at i:56798913 original size:29 final size:25
Alignment explanation
Indices: 56798846--56798914 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 25
56798836 AAATTAAATT
56798846 TTAGTAATCAAAATA-TAAATAAAA
1 TTAGTAATCAAAATATTAAATAAAA
* *
56798870 TTAATAATTAAAATATTACAAAATAAAA
1 TTAGTAATCAAAATATT---AAATAAAA
56798898 TTGAGTAATCAAAATAT
1 TT-AGTAATCAAAATAT
56798915 AATTTAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 13 0.36
25 1 0.03
28 10 0.28
29 12 0.33
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
TTAGTAATCAAAATATTAAATAAAA
Found at i:56805649 original size:31 final size:31
Alignment explanation
Indices: 56805566--56805658 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
56805556 GGGAATTAGT
*
56805566 CATTCATATTTGCATATCCATACCTTGTAATA
1 CATTCATATTTGCATATTCATACCTTGTAA-A
* * * * *
56805598 -ATTCGTGTTTGCAAACTCATACCCTGTAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
* *
56805628 CATTCATATTTACATATTCATATCTTGTAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
56805659 GTCACATTCA
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
30 1 0.02
31 46 0.98
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (31 bp):
CATTCATATTTGCATATTCATACCTTGTAAA
Found at i:56823025 original size:27 final size:27
Alignment explanation
Indices: 56822993--56823047 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
56822983 CCCATTTTTT
* *
56822993 AATAAACATTAAAAAAATTATTTTAAA
1 AATAAAAAATAAAAAAATTATTTTAAA
56823020 AATAAAAAATAAAAAAATTATTTTAAA
1 AATAAAAAATAAAAAAATTATTTTAAA
56823047 A
1 A
56823048 GTATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AATAAAAAATAAAAAAATTATTTTAAA
Found at i:56826992 original size:40 final size:40
Alignment explanation
Indices: 56826887--56827002 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
56826877 GCTTGGACAA
* * * * * *
56826887 AAAACGCCGCTAAAAATCGAGCATTAGCAGCACTTTATGG
1 AAAACGCCGCTAAAGATCAAACATTTGCGGCGCTTTATGG
* *
56826927 AAAACGCCGCTAAAGATCAAGCATTTGTGGCGCTTTATGG
1 AAAACGCCGCTAAAGATCAAACATTTGCGGCGCTTTATGG
*
56826967 AAAACGCTGCTAAAGATCAAACATTTGCGGCGCTTT
1 AAAACGCCGCTAAAGATCAAACATTTGCGGCGCTTT
56827003 TCGGAACACG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCAAACATTTGCGGCGCTTTATGG
Found at i:56827145 original size:23 final size:22
Alignment explanation
Indices: 56827117--56827159 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56827107 GGCGTTTTTG
*
56827117 AAAAAGCACCGCTAAAGGCCTAA
1 AAAAAG-ACCGCTAAAAGCCTAA
*
56827140 AAAAAGGCCGCTAAAAGCCT
1 AAAAAGACCGCTAAAAGCCT
56827160 GTTTTGGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGACCGCTAAAAGCCTAA
Found at i:56829577 original size:25 final size:25
Alignment explanation
Indices: 56829548--56829597 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56829538 ATCTTTTTAG
56829548 TGATTTTGAAATCAAACAAAATCAA
1 TGATTTTGAAATCAAACAAAATCAA
*
56829573 TGATTTTGAAGTCAAACAAAATCAA
1 TGATTTTGAAATCAAACAAAATCAA
56829598 AATAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (25 bp):
TGATTTTGAAATCAAACAAAATCAA
Found at i:56830275 original size:7 final size:7
Alignment explanation
Indices: 56830265--56830306 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
56830255 AACAAAAACA
56830265 AAAATAT
1 AAAATAT
*
56830272 AAAAT-G
1 AAAATAT
56830278 AAAATAT
1 AAAATAT
56830285 AAAATAT
1 AAAATAT
56830292 AAAATAT
1 AAAATAT
56830299 AAAATAT
1 AAAATAT
56830306 A
1 A
56830307 TATAAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (7 bp):
AAAATAT
Found at i:56830275 original size:13 final size:13
Alignment explanation
Indices: 56830247--56830302 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
56830237 AAGATATGAG
*
56830247 AAAACAAAAACA-
1 AAAACAAAAATAT
56830259 AAAACAAAAATAT
1 AAAACAAAAATAT
**
56830272 AAAATGAAAATAT
1 AAAACAAAAATAT
*
56830285 AAAATATAAAATAT
1 AAAACA-AAAATAT
56830299 AAAA
1 AAAA
56830303 TATATATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.29
13 16 0.42
14 11 0.29
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAACAAAAATAT
Found at i:56830281 original size:14 final size:13
Alignment explanation
Indices: 56830259--56830304 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
56830249 AACAAAAACA
*
56830259 AAAACAAAAATAT
1 AAAATAAAAATAT
*
56830272 AAAATGAAAATAT
1 AAAATAAAAATAT
56830285 AAAATATAAAATAT
1 AAAATA-AAAATAT
56830299 AAAATA
1 AAAATA
56830305 TATATAAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (13 bp):
AAAATAAAAATAT
Found at i:56831963 original size:21 final size:21
Alignment explanation
Indices: 56831939--56832001 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
56831929 AATAAAAAGG
56831939 ATAAATTTTAAAACGATGTTA
1 ATAAATTTTAAAACGATGTTA
* *
56831960 ATAAACTCT-AAAC-ATGTTA
1 ATAAATTTTAAAACGATGTTA
56831979 ATAATAATTTTAAATAACGATGT
1 AT-A-AATTTT-AA-AACGATGT
56832002 GTTGTACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 8 0.25
20 5 0.16
21 11 0.34
23 1 0.03
24 3 0.09
25 4 0.12
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (21 bp):
ATAAATTTTAAAACGATGTTA
Found at i:56833325 original size:25 final size:27
Alignment explanation
Indices: 56833296--56833364 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
56833286 AGGCCAGTTA
56833296 GGCTAAGG-T-ATTGGGCTTAG-GTTTG
1 GGCTAAGGTTAATTGGG-TTAGAGTTTG
*
56833321 GGCT-AGGTTAATTGGGTTAGATTTTG
1 GGCTAAGGTTAATTGGGTTAGAGTTTG
56833347 GGCT-AGGTTAATTGGGTT
1 GGCTAAGGTTAATTGGGTT
56833365 TGTAAAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
24 3 0.08
25 9 0.22
26 28 0.70
ACGTcount: A:0.17, C:0.06, G:0.38, T:0.39
Consensus pattern (27 bp):
GGCTAAGGTTAATTGGGTTAGAGTTTG
Found at i:56833335 original size:26 final size:26
Alignment explanation
Indices: 56833305--56833364 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
56833295 AGGCTAAGGT
56833305 ATTGGGCTTAG-GTTTGGGCTAGGTTA
1 ATTGGG-TTAGAGTTTGGGCTAGGTTA
*
56833331 ATTGGGTTAGATTTTGGGCTAGGTTA
1 ATTGGGTTAGAGTTTGGGCTAGGTTA
56833357 ATTGGGTT
1 ATTGGGTT
56833365 TGTAAAAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.17, C:0.05, G:0.37, T:0.42
Consensus pattern (26 bp):
ATTGGGTTAGAGTTTGGGCTAGGTTA
Found at i:56835181 original size:22 final size:23
Alignment explanation
Indices: 56835128--56835183 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
56835118 CCCATTTTTA
* * *
56835128 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
56835151 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
56835173 ATTAAAATTAA
1 ATTAAAATTAA
56835184 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:56835196 original size:16 final size:16
Alignment explanation
Indices: 56835159--56835198 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
56835149 TTAATAAAAT
* *
56835159 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
56835175 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
56835191 TAAAATTA
1 TAAAATTA
56835199 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:56835260 original size:66 final size:67
Alignment explanation
Indices: 56835187--56835329 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 67
56835177 AAATTAATTG
* *
56835187 TTAGTAAAATTATCAAATTATTAATTG-TTCATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
56835251 GA
66 GA
*
56835253 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
56835318 TGA
65 TGA
56835321 TTAGTAAAA
1 TTAGTAAAA
56835330 CAAACTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.37
68 45 0.63
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:56835283 original size:9 final size:9
Alignment explanation
Indices: 56835271--56835298 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56835261 TTTATCAAAT
56835271 TATTAATTG
1 TATTAATTG
56835280 TATTAATTG
1 TATTAATTG
56835289 TATTAATTG
1 TATTAATTG
56835298 T
1 T
56835299 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:56837098 original size:37 final size:37
Alignment explanation
Indices: 56837057--56837193 Score: 274
Period size: 37 Copynumber: 3.7 Consensus size: 37
56837047 TTTGAGTACT
56837057 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
56837094 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
56837131 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
56837168 TCTGATCAAGAAACAAAGTGATAAGT
1 TCTGATCAAGAAACAAAGTGATAAGT
56837194 AAAAATTGCA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 100 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:56838724 original size:29 final size:29
Alignment explanation
Indices: 56838676--56838732 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
56838666 CCGAAATAAA
* * *
56838676 TTAATTTTTCTATTACT-AAATAAATTAAT
1 TTAATTTTTATAGTAATAAAAT-AATTAAT
56838705 TTAATTTTTATAGTAATAAAATAATTAA
1 TTAATTTTTATAGTAATAAAATAATTAA
56838733 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAATTTTTATAGTAATAAAATAATTAAT
Found at i:56855402 original size:35 final size:35
Alignment explanation
Indices: 56855328--56855402 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
56855318 TGAAAATTTT
* * * *
56855328 TCATATATTTAGAGGATCCTATTCCTAAATATGTT
1 TCATATATTTAGAGGATCCAATACCCAAATATGTA
* *
56855363 TCATATATTTAGAGGATTCAATACCCAGAT-TGATA
1 TCATATATTTAGAGGATCCAATACCCAAATATG-TA
56855398 TCATA
1 TCATA
56855403 CTTGAGACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (35 bp):
TCATATATTTAGAGGATCCAATACCCAAATATGTA
Found at i:56856820 original size:24 final size:24
Alignment explanation
Indices: 56856783--56856839 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
56856773 CTGTTGTTGA
*
56856783 AGTTTTCAATTGAAAATGGTTTCTGT
1 AGTTTTC--TTGAAAATGGTTTCTAT
*
56856809 ATTTTTCTTGAAAATGGTTTCTAT
1 AGTTTTCTTGAAAATGGTTTCTAT
56856833 AGTTTTC
1 AGTTTTC
56856840 AATTTGTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 22 0.79
26 6 0.21
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (24 bp):
AGTTTTCTTGAAAATGGTTTCTAT
Found at i:56857906 original size:67 final size:66
Alignment explanation
Indices: 56857798--56857929 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 66
56857788 CAAAAGGTTT
* *
56857798 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTCTGAGTATAATTTGAACCTAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
56857863 G
66 G
*
56857864 TGGTAGTGTTGGCATTGGCATTAGTAAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAA
1 TGGTAGTGTTGGCATTGGCATTAAT-AAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAA
56857929 T
65 T
56857930 CACATTTGAG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
66 24 0.39
67 38 0.61
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.36
Consensus pattern (66 bp):
TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
G
Found at i:56857957 original size:24 final size:24
Alignment explanation
Indices: 56857925--56857970 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
56857915 AATTTGAACC
56857925 CAAATCACATTTGAGGTGATAACT
1 CAAATCACATTTGAGGTGATAACT
56857949 CAAATCACATTTGAGGTGATAA
1 CAAATCACATTTGAGGTGATAA
56857971 ATACTTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (24 bp):
CAAATCACATTTGAGGTGATAACT
Found at i:56858356 original size:102 final size:102
Alignment explanation
Indices: 56858238--56858457 Score: 413
Period size: 102 Copynumber: 2.2 Consensus size: 102
56858228 AATTATATAT
56858238 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
56858303 TTTAGTAAATTCATATAAGAAGATTTAATATTAAGAA
66 TTTAGTAAATTCATATAAGAAGATTTAATATTAAGAA
*
56858340 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATATTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
* *
56858405 TTTAGTTAATTCATATAAGAATATTTAATATTAAGAA
66 TTTAGTAAATTCATATAAGAAGATTTAATATTAAGAA
56858442 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
56858458 ATTTTTATTA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 115 1.00
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (102 bp):
TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATATAAGAAGATTTAATATTAAGAA
Found at i:56858358 original size:29 final size:28
Alignment explanation
Indices: 56858325--56858390 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
56858315 ATATAAGAAG
56858325 ATTTAATATTAAGAATT-TTATTAAATTAT
1 ATTT-ATATTAAGAATTATT-TTAAATTAT
*
56858354 ATTTA-A-TAATAATTATTTTAAATTAT
1 ATTTATATTAAGAATTATTTTAAATTAT
56858380 ATTTTATATTA
1 A-TTTATATTA
56858391 TTATATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 17 0.53
27 7 0.22
28 2 0.06
29 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTATATTAAGAATTATTTTAAATTAT
Found at i:56858718 original size:45 final size:44
Alignment explanation
Indices: 56858639--56858726 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
56858629 ACATCATTCT
*
56858639 ATTCAACCAAACACAAGAATACTATTACGCCTCTATTCTATTAC
1 ATTCAACCAAACACAAGAATACTATTACGCCTCTATTCCATTAC
* * *
56858683 ATTCAACCAAACA-ATTGAATTGCTATTACGTCTCTATTCCATTA
1 ATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTCCATTA
56858727 TAGCGAACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 1 0.03
44 16 0.42
45 21 0.55
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (44 bp):
ATTCAACCAAACACAAGAATACTATTACGCCTCTATTCCATTAC
Found at i:56864693 original size:36 final size:36
Alignment explanation
Indices: 56864648--56864716 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
56864638 TTAGTTTGAG
* *
56864648 TGCTCGAGTAATTTGGTTGAGGATTTAGAGTTCTTT
1 TGCTCGAGTAAGTAGGTTGAGGATTTAGAGTTCTTT
* * *
56864684 TGCTTGAGTAAGTAGGTTGAGGCTTTAGGGTTC
1 TGCTCGAGTAAGTAGGTTGAGGATTTAGAGTTC
56864717 CTTCAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.19, C:0.09, G:0.32, T:0.41
Consensus pattern (36 bp):
TGCTCGAGTAAGTAGGTTGAGGATTTAGAGTTCTTT
Found at i:56869128 original size:12 final size:11
Alignment explanation
Indices: 56869097--56869139 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
56869087 CTTCAATAAG
*
56869097 AATTACAAAAA
1 AATTATAAAAA
*
56869108 AATT-CAAAAA
1 AATTATAAAAA
*
56869118 ATTTATAAAAA
1 AATTATAAAAA
56869129 AATTATAAAAA
1 AATTATAAAAA
56869140 TTTTCAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:56869148 original size:21 final size:22
Alignment explanation
Indices: 56869102--56869149 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
56869092 ATAAGAATTA
56869102 CAAAAAAATTCAAAAAATTTAT
1 CAAAAAAATTCAAAAAATTTAT
56869124 -AAAAAAATT-ATAAAAATTT-T
1 CAAAAAAATTCA-AAAAATTTAT
56869144 CAAAAA
1 CAAAAA
56869150 TTCTAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (22 bp):
CAAAAAAATTCAAAAAATTTAT
Found at i:56871432 original size:21 final size:20
Alignment explanation
Indices: 56871374--56871434 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
56871364 TTTAGACATG
*
56871374 ACAATGTATAAAGAAAAATTT
1 ACAAT-TATAAAGAAATATTT
*
56871395 ATAATTAAATAAA-AAATATTT
1 ACAATT--ATAAAGAAATATTT
56871416 ACAAGTTATAAAGAAATAT
1 ACAA-TTATAAAGAAATAT
56871435 ATAAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 6 0.18
21 20 0.61
22 7 0.21
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (20 bp):
ACAATTATAAAGAAATATTT
Found at i:56871717 original size:3 final size:3
Alignment explanation
Indices: 56871702--56871758 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
56871692 GATATCGACG
*
56871702 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56871750 ATA A-A ATA A
1 ATA ATA ATA A
56871759 AACACAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56875054 original size:13 final size:13
Alignment explanation
Indices: 56875036--56875063 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56875026 CTTTTGAGTT
56875036 AAAACAAAAAATA
1 AAAACAAAAAATA
56875049 AAAACAAAAAATA
1 AAAACAAAAAATA
56875062 AA
1 AA
56875064 GAACTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAACAAAAAATA
Found at i:56875449 original size:12 final size:12
Alignment explanation
Indices: 56875438--56875484 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
56875428 TTTAGCTTAT
56875438 TTAGT-TTATTA
1 TTAGTATTATTA
*
56875449 TTATTATTATTA
1 TTAGTATTATTA
*
56875461 TTAGTGTTATTA
1 TTAGTATTATTA
* *
56875473 TCATTATTATTA
1 TTAGTATTATTA
56875485 CTATTATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
11 4 0.14
12 25 0.86
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (12 bp):
TTAGTATTATTA
Found at i:56875451 original size:3 final size:3
Alignment explanation
Indices: 56875443--56875503 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
56875433 CTTATTTAGT
* * * *
56875443 TTA TTA TTA TTA TTA TTA TTA GTG TTA TTA TCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
56875491 TTAA CTA TTA TTA
1 TT-A TTA TTA TTA
56875504 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:56876311 original size:108 final size:110
Alignment explanation
Indices: 56876115--56876337 Score: 326
Period size: 108 Copynumber: 2.0 Consensus size: 110
56876105 TTTCTAATTG
*
56876115 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
*
56876180 TCGTTCAACAAAATAGTTAAATATCCTTTTAAAA-TTTTAAAATA
66 TCATTCAACAAAATAGTTAAATATCCTTTTAAAACTTTTAAAATA
* * * *
56876224 AGGCAATGTTTTGCGTTT-GGAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTC
1 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * * *
56876288 TCATTCAACCAAATGGCTT-AATATCCTTTTAAAACTTTTCACATA
66 TCATTCAACAAAATAG-TTAAATATCCTTTTAAAACTTTTAAAATA
56876333 AGGCA
1 AGGCA
56876338 CCTGGGTGTC
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
108 71 0.70
109 31 0.30
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (110 bp):
AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
TCATTCAACAAAATAGTTAAATATCCTTTTAAAACTTTTAAAATA
Found at i:56876494 original size:181 final size:176
Alignment explanation
Indices: 56876163--56876495 Score: 497
Period size: 181 Copynumber: 1.9 Consensus size: 176
56876153 CCCTAAGGTG
*
56876163 CTGGGTGTCGATTTTTCTCGTTCAACAAAATAGTTAAATATCCTTTTAAAATTTTAAAATAAGGC
1 CTGGGTGTCGATTTTTCTCGTTCAACAAAATAGCTAAATATCCTTTTAAAATTTTAAAATAAGGC
* *
56876228 AATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTCTCATT
66 AATGTTTTGCATTTGGAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTATCATT
* **
56876293 CAACCAAATGGCTTAATATCCTTTTAAAACTTTTCACATAAGGCAC
131 CAACCAAATAGCCAAATATCCTTTTAAAACTTTTCACATAAGGCAC
* * *
56876339 CTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTTTCGAAATA
1 CTGGGTGTCGATTTTTCTCGTTCAACAAAATAGCTAAATATCCTTTT-AAAA--TTTT-AAAATA
* *
56876404 AGGCAATGTTTTGTATTTGGGAAATTCGA-GAGAACGTGCCCTAAGGTGTTGGGTGTCGATTTTT
62 AGGCAATGTTTTGCATTT-GGAAATTCGAGGA-AACATGCCCTAAGGTGTTGGGTGTCGATTTTT
*
56876468 ATCATTTAACCAAATAGCCAAATATCCT
125 ATCATTCAACCAAATAGCCAAATATCCT
56876496 CTTGAATTTC
Statistics
Matches: 139, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
176 44 0.32
177 4 0.03
179 4 0.03
180 23 0.17
181 64 0.46
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (176 bp):
CTGGGTGTCGATTTTTCTCGTTCAACAAAATAGCTAAATATCCTTTTAAAATTTTAAAATAAGGC
AATGTTTTGCATTTGGAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTATCATT
CAACCAAATAGCCAAATATCCTTTTAAAACTTTTCACATAAGGCAC
Found at i:56879028 original size:210 final size:210
Alignment explanation
Indices: 56878666--56879083 Score: 836
Period size: 210 Copynumber: 2.0 Consensus size: 210
56878656 GCTTGGAAAC
56878666 GAATTCACCAGATGAAAAGAATTGTCGTAGGAGCAACTACAACTCCCGAATATCACGGGTGGCGA
1 GAATTCACCAGATGAAAAGAATTGTCGTAGGAGCAACTACAACTCCCGAATATCACGGGTGGCGA
56878731 AGTAAGAGGATCGATGATAACATCCCAAAGCCAAGAGAAGAATGTGGTCGTCCTATAGAAGAACA
66 AGTAAGAGGATCGATGATAACATCCCAAAGCCAAGAGAAGAATGTGGTCGTCCTATAGAAGAACA
56878796 TTTACGAGTAGCCCCTTCAGAATTAGAGATCATCAAGCAAGACTTCGAAAAAAGAAGTTCAGAGT
131 TTTACGAGTAGCCCCTTCAGAATTAGAGATCATCAAGCAAGACTTCGAAAAAAGAAGTTCAGAGT
56878861 TTGGAAAGAGGATGT
196 TTGGAAAGAGGATGT
56878876 GAATTCACCAGATGAAAAGAATTGTCGTAGGAGCAACTACAACTCCCGAATATCACGGGTGGCGA
1 GAATTCACCAGATGAAAAGAATTGTCGTAGGAGCAACTACAACTCCCGAATATCACGGGTGGCGA
56878941 AGTAAGAGGATCGATGATAACATCCCAAAGCCAAGAGAAGAATGTGGTCGTCCTATAGAAGAACA
66 AGTAAGAGGATCGATGATAACATCCCAAAGCCAAGAGAAGAATGTGGTCGTCCTATAGAAGAACA
56879006 TTTACGAGTAGCCCCTTCAGAATTAGAGATCATCAAGCAAGACTTCGAAAAAAGAAGTTCAGAGT
131 TTTACGAGTAGCCCCTTCAGAATTAGAGATCATCAAGCAAGACTTCGAAAAAAGAAGTTCAGAGT
56879071 TTGGAAAGAGGAT
196 TTGGAAAGAGGAT
56879084 AGAACAGCTA
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 208 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (210 bp):
GAATTCACCAGATGAAAAGAATTGTCGTAGGAGCAACTACAACTCCCGAATATCACGGGTGGCGA
AGTAAGAGGATCGATGATAACATCCCAAAGCCAAGAGAAGAATGTGGTCGTCCTATAGAAGAACA
TTTACGAGTAGCCCCTTCAGAATTAGAGATCATCAAGCAAGACTTCGAAAAAAGAAGTTCAGAGT
TTGGAAAGAGGATGT
Found at i:56888506 original size:46 final size:45
Alignment explanation
Indices: 56888454--56888838 Score: 187
Period size: 46 Copynumber: 8.7 Consensus size: 45
56888444 TCGCATCAGG
* *
56888454 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAA-TTCAAA
* * *
56888500 TCTTATCT-CCTCG-AGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCT-GAAG-TTACAGTGGAGCAGACCGAAGAATTCA-AA
* * ** *
56888543 TCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AA-TAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATTCAA--A
* * * * * **
56888587 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GTA-TCAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATTCAAA
* * * *
56888628 TCTTATCTCCCTGAGGTTACACTGGAGTAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAA-TTCAAA
* * * * *
56888674 TCTTATCTCCCCG-AGATTATAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGACCGAAGAATTCA-AA
* * * * ** *
56888717 TCCTATCTCCCTGAAGTTATAGTAGAGCGGA-TTAA-AA-TAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATTCAA--A
* * ** *
56888761 TCTTATCTCTCTGAAGTTACAGTGGAGTAGACCGATCAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAA-TTCAAA
56888807 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAC
56888839 TAAGACCACA
Statistics
Matches: 253, Mismatches: 59, Indels: 54
0.69 0.16 0.15
Matches are distributed among these distances:
41 28 0.11
42 10 0.04
43 51 0.20
44 62 0.25
45 8 0.03
46 92 0.36
48 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATTCAAA
Found at i:56888592 original size:87 final size:87
Alignment explanation
Indices: 56888499--56888769 Score: 282
Period size: 87 Copynumber: 3.1 Consensus size: 87
56888489 AGAATTTCAA
56888499 ATCTTATCTCCTCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACA
1 ATCTTATCTCCTCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACA
56888564 GTGGAGCGGATTAAAATAAAGG
66 GTGGAGCGGATTAAAATAAAGG
** * * * ** * *
56888586 ATCTTATCT-CTCTGA-AGTTACAGTAGAGTAGATCGTA-TCA-GGTCTTATCTCCCTGAGGTTA
1 ATCTTATCTCCTC-GAGA-TTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
* ** ** **
56888647 CACTGGAGTAGACCGAAGAATTTCA-G
64 CAGTGGAGCGGA-TTAA-AA-TAAAGG
* * *
56888673 ATCTTATCTCCCCGAGATTATAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTATA
1 ATCTTATCTCCTCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACA
*
56888738 GTAGAGCGGATTAAAATAAAGG
66 GTGGAGCGGATTAAAATAAAGG
56888760 ATCTTATCTC
1 ATCTTATCTC
56888770 TCTGAAGTTA
Statistics
Matches: 138, Mismatches: 36, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
85 26 0.19
86 10 0.07
87 69 0.50
88 9 0.07
89 24 0.17
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (87 bp):
ATCTTATCTCCTCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACA
GTGGAGCGGATTAAAATAAAGG
Found at i:56888700 original size:174 final size:174
Alignment explanation
Indices: 56888408--56888838 Score: 700
Period size: 174 Copynumber: 2.4 Consensus size: 174
56888398 AGTGAATATT
* *
56888408 AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTATATCGCATCAGGTCTTATCTCCCTGAGGTTA
1 AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGGTTA
*
56888473 CAGTGGAGTAGACCGAAGAATTTCAAATCTTATCTCCTCGAGATTACAGCGGAGCAGATCGAAGA
66 CAGTGGAGTAGACCGAAGAATTTCAAATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGA
*
56888538 CACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATA
131 CACTATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATA
56888582 AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGGTTA
1 AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGGTTA
* * *
56888647 CACTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCCGAGATTATAGCGGAGCAGATCGAAGA
66 CAGTGGAGTAGACCGAAGAATTTCAAATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGA
*
56888712 CACTATCCTATCTCCCTGAAGTTATAGTAGAGCGGATTAAAATA
131 CACTATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATA
* * *
56888756 AAGGATCTTATCTCTCTGAAGTTACAGTGGAGTAGACCGATCAATTTCAGATCTTATCTCCCTGA
1 AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG-T--A--TCAGGTCTTATCTCCCTGA
* *
56888821 AGTTACAGTGGAGCAGAC
61 GGTTACAGTGGAGTAGAC
56888839 TAAGACCACA
Statistics
Matches: 238, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
174 203 0.85
175 1 0.00
177 1 0.00
179 33 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (174 bp):
AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGGTTA
CAGTGGAGTAGACCGAAGAATTTCAAATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGA
CACTATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATA
Found at i:56890348 original size:3 final size:3
Alignment explanation
Indices: 56890340--56890397 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
56890330 CTTATTTAGT
* * * *
56890340 TTA TTA TTA TTA TTA TTA GTG TTA TTA TCA TTA TTA TTA CTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
56890389 CTA TTA TTA
1 TTA TTA TTA
56890398 ATTTTATTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:56890355 original size:21 final size:22
Alignment explanation
Indices: 56890331--56890377 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
56890321 ATGATTTAGC
*
56890331 TTATTTAGT-TTATTATTATTA
1 TTATTTAGTGTTATTATCATTA
56890352 TTA-TTAGTGTTATTATCATTA
1 TTATTTAGTGTTATTATCATTA
56890373 TTATT
1 TTATT
56890378 ACTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (22 bp):
TTATTTAGTGTTATTATCATTA
Found at i:56891385 original size:114 final size:110
Alignment explanation
Indices: 56891010--56891429 Score: 585
Period size: 114 Copynumber: 3.8 Consensus size: 110
56891000 TTTCTAATTG
* * * *
56891010 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCATTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * * *
56891075 TCGTTCAACAAAATAGTTAAATATCCTTTT-AAAATTTTAAAATA
66 TCATTCAACCAAATAGCTAAATATCCTTTTAAAAATTTTCAAATA
* * * *
56891119 AGGCAATGTTTTGCGTTT-GGAAATTCGAG-GAAACATGCCCTAAGGTGTTGGATGTCGATTTTT
1 AGGCAATGTTTTGCATTTGGGAAATTCGAGAG-AACGTGCCCTAAGGTGCTGGGTGTCGATTTTT
* * *
56891182 CTCATTCAACCAAATGGCTTAATATCCTTTTAAAACTTTTCAAATA
65 CTCATTCAACCAAATAGCTAAATATCCTTTTAAAAATTTTCAAATA
56891228 AGGCAATGTTTTGCATTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCATTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* *
56891293 TCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAAAATTTTCGAAATA
66 TCATTCAACCAAATAGCTAAATATCCTTTT---AAAAATTTTC-AAATA
* *
56891342 AGGCAATGTTTTGCATTTGAGAAATTTGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCATTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* *
56891407 TCATTTAACCAAATAGCCAAATA
66 TCATTCAACCAAATAGCTAAATA
56891430 GCCAAATATC
Statistics
Matches: 277, Mismatches: 26, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
108 66 0.24
109 45 0.16
110 69 0.25
111 1 0.00
113 9 0.03
114 87 0.31
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (110 bp):
AGGCAATGTTTTGCATTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
TCATTCAACCAAATAGCTAAATATCCTTTTAAAAATTTTCAAATA
Found at i:56891977 original size:2 final size:2
Alignment explanation
Indices: 56891970--56891996 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56891960 GCCTATTCTC
56891970 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
56891997 ATTTAACCAA
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:56897856 original size:28 final size:29
Alignment explanation
Indices: 56897800--56897861 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
56897790 CATAAATATT
*
56897800 ATAAAAAATAATTACCAAAATGAGATAAA
1 ATAAAAAATAAATACCAAAATGAGATAAA
* * * *
56897829 TTAAAAATTAAATACGAAAAT-AGGTAAA
1 ATAAAAAATAAATACCAAAATGAGATAAA
56897857 ATAAA
1 ATAAA
56897862 TAGCTTGCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.23
Consensus pattern (29 bp):
ATAAAAAATAAATACCAAAATGAGATAAA
Found at i:56898024 original size:29 final size:28
Alignment explanation
Indices: 56897991--56898051 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
56897981 AAACGCCCAT
56897991 TTTTTTAAAAAATTACCGAAATGGGCTCG
1 TTTTTTAAAAAATTACCGAAATGGGC-CG
** * *
56898020 TTTTTTAATTATTTACCGGAATGGGCCG
1 TTTTTTAAAAAATTACCGAAATGGGCCG
56898048 TTTT
1 TTTT
56898052 CCGCGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (28 bp):
TTTTTTAAAAAATTACCGAAATGGGCCG
Found at i:56898300 original size:23 final size:21
Alignment explanation
Indices: 56898262--56898331 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
56898252 AAATTCAATA
* *
56898262 TCAATATCCTTCAAAATTTCTT
1 TCAAT-TCCTTCAAAAATTCTC
56898284 TCAATTCCGTTCAAAAATTCTC
1 TCAATTCC-TTCAAAAATTCTC
56898306 TCAAATTCCTTTC-AAAATTCTC
1 TC-AATTCC-TTCAAAAATTCTC
56898328 TCAA
1 TCAA
56898332 ACTCTCAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.12
22 29 0.67
23 9 0.21
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.40
Consensus pattern (21 bp):
TCAATTCCTTCAAAAATTCTC
Found at i:56898332 original size:22 final size:22
Alignment explanation
Indices: 56898271--56898332 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
56898261 ATCAATATCC
*
56898271 TTCAAAATTTCTTTC-AATTCCG
1 TTCAAAA-TTCTCTCAAATTCCG
*
56898293 TTCAAAAATTCTCTCAAATTCCT
1 TTC-AAAATTCTCTCAAATTCCG
56898316 TTCAAAATTCTCTCAAA
1 TTCAAAATTCTCTCAAA
56898333 CTCTCAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 23 0.64
23 13 0.36
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (22 bp):
TTCAAAATTCTCTCAAATTCCG
Found at i:56898339 original size:30 final size:30
Alignment explanation
Indices: 56898303--56898361 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
56898293 TTCAAAAATT
* * *
56898303 CTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAAATGCCTTCCAAAATCCTCTCAAA
56898333 CTCTCAAATGCCTTCCAAAATCCTCTCAA
1 CTCTCAAATGCCTTCCAAAATCCTCTCAA
56898362 TTTCCTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (30 bp):
CTCTCAAATGCCTTCCAAAATCCTCTCAAA
Found at i:56898481 original size:29 final size:29
Alignment explanation
Indices: 56898418--56898481 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
56898408 TAAATTTCAT
* *
56898418 TATTTTAAGAAAATTTTAAAATTTTTTAT
1 TATTTTAAAAAAATTTTAAAATTTTTTAA
*
56898447 TTTTTTAAAAATAATTTTAAAA-TTTTTAA
1 TATTTTAAAAA-AATTTTAAAATTTTTTAA
56898476 TATTTT
1 TATTTT
56898482 CAACAATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TATTTTAAAAAAATTTTAAAATTTTTTAA
Found at i:56901106 original size:28 final size:28
Alignment explanation
Indices: 56901061--56901559 Score: 517
Period size: 28 Copynumber: 17.9 Consensus size: 28
56901051 TTTTGACATT
*
56901061 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
56901089 ATATAATTAAAAA--C---CCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
56901112 ACTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
56901140 ATTTAATTAAAAA---T--CCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
56901163 ACTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
*
56901192 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
56901220 ATTTAATTAAAAACCCTAATCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
56901248 ATTTAATTAAAAACCCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
56901276 ATTTAATTAAAAACCCTAACTTAAACCTATA
1 ATTTAATTAAAAACCCTAACCT-AA-CT-TA
*
56901307 ATTTAATTTAATTAAA----AACCCTAACATA
1 ATTTAA-TTAA--AAACCCTAA-CCTAACTTA
* *
56901335 ATTTAGTTAAAAACCCTAATCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* * *
56901364 TTTTACA-TGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAA-CCTAACTTA
*
56901393 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
56901421 ATTTAATTAAAAACCCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
56901449 ATTTAATTAAAAACCCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
56901477 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* * *
56901506 TTTTACA-TGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAA-CCTAACTTA
56901535 ATTTAATTAAAAACCCTAACCTAAC
1 ATTTAATTAAAAACCCTAACCTAAC
56901560 NNNNNNNNNN
Statistics
Matches: 406, Mismatches: 38, Indels: 54
0.82 0.08 0.11
Matches are distributed among these distances:
23 40 0.10
25 5 0.01
26 2 0.00
27 4 0.01
28 208 0.51
29 124 0.31
30 6 0.01
31 10 0.02
32 4 0.01
34 3 0.01
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:56904964 original size:124 final size:124
Alignment explanation
Indices: 56904744--56904981 Score: 379
Period size: 124 Copynumber: 1.9 Consensus size: 124
56904734 CCACGAGGGC
* *
56904744 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACATCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * *
56904809 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTTATATAGCATTCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATTCTGGTATCA
* * *
56904868 GCGATTTTATACTATTTGCTCAGAAAACATCAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTGCTCAG-AAACATCAAAAAAAATTATTTCCTACATGACCAACTGTAGC
56904932 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCAT
65 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCAT
56904982 CCTAGTAGAA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
124 75 0.72
125 29 0.28
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACATCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATTCTGGTATCA
Found at i:56905016 original size:27 final size:27
Alignment explanation
Indices: 56904974--56905027 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
56904964 TTTCTTCTCA
56904974 AATAGCATCCTAGTAGAAGCGATTTCC
1 AATAGCATCCTAGTAGAAGCGATTTCC
*
56905001 AATAGCATCCTGGTAGAAGCGATTTCC
1 AATAGCATCCTAGTAGAAGCGATTTCC
56905028 CACTATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (27 bp):
AATAGCATCCTAGTAGAAGCGATTTCC
Found at i:56914859 original size:9 final size:9
Alignment explanation
Indices: 56914845--56914873 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
56914835 TCTTGTACCT
56914845 TGTAAGAAA
1 TGTAAGAAA
56914854 TGTAAGAAA
1 TGTAAGAAA
56914863 TGTAAGAAA
1 TGTAAGAAA
56914872 TG
1 TG
56914874 AAACATGATT
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (9 bp):
TGTAAGAAA
Found at i:56918458 original size:15 final size:15
Alignment explanation
Indices: 56918438--56918469 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56918428 CTGGTTCTGA
56918438 AACGGAATTTGGAAG
1 AACGGAATTTGGAAG
56918453 AACGGAATTTGGAAG
1 AACGGAATTTGGAAG
56918468 AA
1 AA
56918470 AGAGAGCCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (15 bp):
AACGGAATTTGGAAG
Found at i:56919342 original size:13 final size:13
Alignment explanation
Indices: 56919320--56919351 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56919310 GTAAAAATAT
56919320 ATTAAAATGCACA
1 ATTAAAATGCACA
*
56919333 ATTAATATGCACA
1 ATTAAAATGCACA
56919346 ATTAAA
1 ATTAAA
56919352 TTATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (13 bp):
ATTAAAATGCACA
Found at i:56919677 original size:34 final size:34
Alignment explanation
Indices: 56919634--56919700 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
56919624 TTGGCAATTT
56919634 GTTGACTAGCACTACACCCAAAAAAATTATTTTG
1 GTTGACTAGCACTACACCCAAAAAAATTATTTTG
* *
56919668 GTTGACTAGCACTACACTCAAAAATATTATTTT
1 GTTGACTAGCACTACACCCAAAAAAATTATTTT
56919701 TTAATCAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (34 bp):
GTTGACTAGCACTACACCCAAAAAAATTATTTTG
Found at i:56927933 original size:14 final size:14
Alignment explanation
Indices: 56927914--56927944 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56927904 GGAATTGTTA
*
56927914 TAATCTAAATTTAC
1 TAATCTAAATTAAC
56927928 TAATCTAAATTAAC
1 TAATCTAAATTAAC
56927942 TAA
1 TAA
56927945 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:56930710 original size:25 final size:25
Alignment explanation
Indices: 56930651--56930710 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 25
56930641 TTGTGAATTT
*
56930651 TATTTTATTAGTATTTTATATTTAAA
1 TATTTT-TTAGTATTATATATTTAAA
56930677 -ATTGATTTTA-TATTATATATATTAAA
1 TATT--TTTTAGTATTATATAT-TTAAA
56930703 TATTTTTT
1 TATTTTTT
56930711 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
25 16 0.55
26 8 0.28
27 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TATTTTTTAGTATTATATATTTAAA
Found at i:56932976 original size:7 final size:7
Alignment explanation
Indices: 56932961--56933015 Score: 92
Period size: 7 Copynumber: 7.9 Consensus size: 7
56932951 ATAACCCGAT
56932961 CCCTAAC
1 CCCTAAC
*
56932968 CCTTAAC
1 CCCTAAC
56932975 CCCTAAC
1 CCCTAAC
56932982 CCCTAAC
1 CCCTAAC
56932989 CCCTAAC
1 CCCTAAC
*
56932996 CCTTAAC
1 CCCTAAC
56933003 CCCTAAC
1 CCCTAAC
56933010 CCCTAA
1 CCCTAA
56933016 ACCTTATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAC
Found at i:56933658 original size:114 final size:114
Alignment explanation
Indices: 56933452--56934017 Score: 855
Period size: 114 Copynumber: 5.0 Consensus size: 114
56933442 TTTTAAATCT
* **
56933452 CTGAGTATTAGCGGCGCTTACATAAAAACGCCACTAAATCC-TCGAAAGCTCAGAAAACGGCGTC
1 CTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTTC-TCAGCTCAGAAAACGGCGTC
* *
56933516 GTTGGGCTGAAGTATTTTTACGGTGCTTTCCCAAAAACGCCGCTAAAGAC
65 GTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGAC
* * *
56933566 TTGAGCATTAGCGGCGCTTACATAAAAATGCCACTAAATCCTTCTCAGCTCAGAAAACGGTGTCG
1 CTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTTCTCAGCTCAGAAAACGGCGTCG
* *
56933631 TTGGGGTGAAGTATTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGAC
66 TTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGAC
* * * *
56933680 CTGAACATTAGTGGCGCTTACATAAAAACACCACTAAATCCTTCTTAGCTCAGAAAACGGCGTCG
1 CTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTTCTCAGCTCAGAAAACGGCGTCG
* ** *
56933745 TTAGATTGACGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGAC
66 TTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGAC
* * *
56933794 CTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCTTATCAACTCAGAAAACGGCGTCG
1 CTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTTCTCAGCTCAGAAAACGGCGTCG
*
56933859 TTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAGAACGCCGCTAAAGAC
66 TTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGAC
* ** * *
56933908 CTGACCAGCAGCGGCACTTACATAAAAATGCCACTAAATCCTTCTCAGCTCAGAAAACGGCGTCG
1 CTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTTCTCAGCTCAGAAAACGGCGTCG
* *
56933973 TTGGGCTGAAGTATTTTTGCGACGCTTTCCCAAAAATGCCGCTAA
66 TTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAA
56934018 TGCTTATTTT
Statistics
Matches: 406, Mismatches: 45, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
114 404 1.00
115 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (114 bp):
CTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTTCTCAGCTCAGAAAACGGCGTCG
TTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGAC
Found at i:56935235 original size:43 final size:45
Alignment explanation
Indices: 56935120--56935238 Score: 125
Period size: 43 Copynumber: 2.7 Consensus size: 45
56935110 AAAAAAGAGT
* * *
56935120 AACAATTCCTTAAAAACTAGCCTAGAAAACGTGGATGACTAGAAAA
1 AACAAATCCCTAAAAACTAGCCTA-AAAATGTGGATGACTAGAAAA
* ** * * * *
56935166 AACAAATCCCTGAAATGTAACTTAAAAATGTGGATGGCTA-AGAA
1 AACAAATCCCTAAAAACTAGCCTAAAAATGTGGATGACTAGAAAA
56935210 AA-AAATCCCTAAAAACTAGCCTAAAAATG
1 AACAAATCCCTAAAAACTAGCCTAAAAATG
56935239 CGGGTAGTTA
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
43 22 0.38
44 5 0.09
45 14 0.24
46 17 0.29
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (45 bp):
AACAAATCCCTAAAAACTAGCCTAAAAATGTGGATGACTAGAAAA
Found at i:56943000 original size:11 final size:11
Alignment explanation
Indices: 56942984--56943022 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
56942974 CTTTTCCTTT
*
56942984 AATCAAACAAG
1 AATCAAGCAAG
56942995 AATCAAGCTAA-
1 AATCAAGC-AAG
56943006 AATCAAGCAAG
1 AATCAAGCAAG
56943017 AATCAA
1 AATCAA
56943023 CCTCTTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.13
Consensus pattern (11 bp):
AATCAAGCAAG
Found at i:56946775 original size:3 final size:3
Alignment explanation
Indices: 56946758--56946828 Score: 124
Period size: 3 Copynumber: 23.3 Consensus size: 3
56946748 TCCAAAGAGA
*
56946758 AAG AAG AATG TAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
56946804 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
56946829 GAGTAATTAG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 63 0.97
4 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:56949584 original size:19 final size:19
Alignment explanation
Indices: 56949562--56949602 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
56949552 TCAATTTGAA
56949562 AAAAAAC-AGAAAATTTTG
1 AAAAAACTAGAAAATTTTG
* *
56949580 GAAAAACTTGAAAATTTTG
1 AAAAAACTAGAAAATTTTG
56949599 AAAA
1 AAAA
56949603 CATGGTCACG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (19 bp):
AAAAAACTAGAAAATTTTG
Found at i:56949586 original size:18 final size:18
Alignment explanation
Indices: 56949563--56949602 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
56949553 CAATTTGAAA
56949563 AAAAAC-AGAAAATTTTGG
1 AAAAACTAGAAAATTTT-G
*
56949581 AAAAACTTGAAAATTTTG
1 AAAAACTAGAAAATTTTG
56949599 AAAA
1 AAAA
56949603 CATGGTCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (18 bp):
AAAAACTAGAAAATTTTG
Found at i:56953660 original size:44 final size:44
Alignment explanation
Indices: 56953612--56953727 Score: 205
Period size: 44 Copynumber: 2.6 Consensus size: 44
56953602 AATGTCATTG
*
56953612 TATCTTTCAACCATGTTCTTTCCTTTTTGAATATAATGCCATGA
1 TATCTTTCAATCATGTTCTTTCCTTTTTGAATATAATGCCATGA
56953656 TATCTTTCAATCATGTTCTTTCCTTTTTGAATATAATGCCATGA
1 TATCTTTCAATCATGTTCTTTCCTTTTTGAATATAATGCCATGA
* *
56953700 TATCTTTCAATCATGGTCTTTCCCTTTT
1 TATCTTTCAATCATGTTCTTTCCTTTTT
56953728 CTCAAATCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.22, C:0.21, G:0.09, T:0.48
Consensus pattern (44 bp):
TATCTTTCAATCATGTTCTTTCCTTTTTGAATATAATGCCATGA
Found at i:56955652 original size:16 final size:16
Alignment explanation
Indices: 56955628--56955658 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56955618 AGAAATTCCA
*
56955628 AAGAGAAAGAAGAAGG
1 AAGAAAAAGAAGAAGG
56955644 AAGAAAAAGAAGAAG
1 AAGAAAAAGAAGAAG
56955659 AGAGTAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAGAAGG
Found at i:56960342 original size:43 final size:43
Alignment explanation
Indices: 56960285--56960570 Score: 328
Period size: 43 Copynumber: 6.7 Consensus size: 43
56960275 ATTTTTAGAA
*
56960285 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTCTCCC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCC
* * *
56960328 ACAAACGCCACTAAAG-ACTAAGACCATTAGTGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGAAC-AAGACCTTTAGCGGCGCTTTTCCC
* * *
56960371 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCC
* * * *
56960414 ACAAACGCCGCTAAAGACCAAGACCATTAGCGACGCTTTTTCC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCC
*
56960457 ACAAACGCCACTAAAG-ACAAAGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGAAC-AAGACCTTTAGCGGCGCTTTTCCC
* * ** * * *
56960500 ACAAACGCTGCTAAAGACCGTGACTTTTAGCGGCGCTTCTCGC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCC
* *
56960543 AAAAACACCGCTAAA-AACATA-ACCTTTA
1 ACAAACGCCGCTAAAGAACA-AGACCTTTA
56960571 AAAAATATAT
Statistics
Matches: 203, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
42 11 0.05
43 190 0.94
44 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCC
Found at i:56960481 original size:129 final size:129
Alignment explanation
Indices: 56960285--56960561 Score: 412
Period size: 129 Copynumber: 2.2 Consensus size: 129
56960275 ATTTTTAGAA
* * *
56960285 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTCTCCCACAAACGCCACTAAAGACTAAG
1 ACAAACGCCGCTAAAGAACAAGACCATTAGCGACGCTTCTCCCACAAACGCCACTAAAGACAAAG
* * *
56960350 ACCATTAGTGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTC
66 ACCATTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCGC
* * *
56960414 ACAAACGCCGCTAAAGACCAAGACCATTAGCGACGCTTTTTCCACAAACGCCACTAAAGACAAAG
1 ACAAACGCCGCTAAAGAACAAGACCATTAGCGACGCTTCTCCCACAAACGCCACTAAAGACAAAG
* * * *
56960479 ACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGACCGTGACTTTTAGCGGCGCTTCTCGC
66 ACCATTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCGC
* *
56960543 AAAAACACCGCTAAA-AACA
1 ACAAACGCCGCTAAAGAACA
56960562 TAACCTTTAA
Statistics
Matches: 132, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
128 3 0.02
129 129 0.98
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (129 bp):
ACAAACGCCGCTAAAGAACAAGACCATTAGCGACGCTTCTCCCACAAACGCCACTAAAGACAAAG
ACCATTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCGC
Found at i:56962094 original size:23 final size:25
Alignment explanation
Indices: 56962068--56962117 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
56962058 CAGTTGATAA
56962068 AACCA-ATA-ATATGATCAAATTAT
1 AACCACATACATATGATCAAATTAT
*
56962091 AACCACTTACATATGATCAAATTAT
1 AACCACATACATATGATCAAATTAT
56962116 AA
1 AA
56962118 ATCAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 2 0.08
25 17 0.71
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (25 bp):
AACCACATACATATGATCAAATTAT
Found at i:56972669 original size:50 final size:50
Alignment explanation
Indices: 56972554--56972746 Score: 287
Period size: 50 Copynumber: 3.8 Consensus size: 50
56972544 GATCATAACA
* ** *
56972554 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
56972605 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
56972655 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
56972705 TGTCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56972747 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 96 0.74
51 34 0.26
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:56972862 original size:13 final size:13
Alignment explanation
Indices: 56972841--56972870 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56972831 GCTTGGGTCA
56972841 TCATCAAATAAAT
1 TCATCAAATAAAT
*
56972854 TCATGAAATAAAT
1 TCATCAAATAAAT
56972867 TCAT
1 TCAT
56972871 AGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:56976343 original size:13 final size:14
Alignment explanation
Indices: 56976325--56976365 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
56976315 TTTTCAAAGA
56976325 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
56976338 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
56976352 TACGGTTTA-GACT
1 TATGGTTTAGGACT
56976365 T
1 T
56976366 TAAGGGTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:56976456 original size:25 final size:26
Alignment explanation
Indices: 56976422--56976473 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
56976412 TTGTTTGTGG
** *
56976422 TTTACGGGTTTAATTTTTATGGTTAA
1 TTTACGGGTTTAAGATTTACGGTTAA
56976448 TTTA-GGGTTTAAGATTTACGGTTAA
1 TTTACGGGTTTAAGATTTACGGTTAA
56976473 T
1 T
56976474 GCGTACGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (26 bp):
TTTACGGGTTTAAGATTTACGGTTAA
Found at i:56977820 original size:16 final size:16
Alignment explanation
Indices: 56977799--56977854 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
56977789 ACTTAGTAAT
56977799 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
*
56977815 TAAAAGATACACTTAA
1 TAAAAGATACAATTAA
* * *
56977831 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
56977847 TAAAAGAT
1 TAAAAGAT
56977855 GTGAGTTTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 3 0.09
16 25 0.78
17 4 0.12
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:56978902 original size:47 final size:47
Alignment explanation
Indices: 56978833--56978926 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
56978823 TGCTTCGATT
*
56978833 CCCCTTCCAAAAGATAATTTAGGGCTTGATTAATGCATATGGAGGTG
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
* * * *
56978880 CCCCTTCTAAAATATAATTTAGGATTTGATTAATGCATGTGGAGGTG
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
56978927 GTCTAGCGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (47 bp):
CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
Found at i:56979432 original size:9 final size:9
Alignment explanation
Indices: 56979418--56979599 Score: 101
Period size: 9 Copynumber: 19.6 Consensus size: 9
56979408 ATTAATATTA
*
56979418 TACATAAAT
1 TACATAACT
56979427 TACATAACT
1 TACATAACT
56979436 TA-ATTAA-T
1 TACA-TAACT
*
56979444 TA-AT-ATT
1 TACATAACT
56979451 ATACATAACT
1 -TACATAACT
56979461 TACATAACT
1 TACATAACT
56979470 TAC--AACT
1 TACATAACT
56979477 TACATAACT
1 TACATAACT
*
56979486 TACATTAATAT
1 TACA-TAA-CT
* *
56979497 TACACATATT
1 TACATA-ACT
56979507 ATACATAACT
1 -TACATAACT
56979517 TAC--AACT
1 TACATAACT
56979524 TACATAACT
1 TACATAACT
*
56979533 TACATTAATATT
1 TACA-T-A-ACT
*
56979545 ATACATAAAT
1 -TACATAACT
56979555 TACATAACT
1 TACATAACT
*
56979564 TACATTAATATT
1 TACA-T-A-ACT
*
56979576 ATACATAAAT
1 -TACATAACT
56979586 TACATAACT
1 TACATAACT
56979595 TACAT
1 TACAT
56979600 TAATACGACA
Statistics
Matches: 139, Mismatches: 13, Indels: 42
0.72 0.07 0.22
Matches are distributed among these distances:
6 1 0.01
7 16 0.12
8 7 0.05
9 71 0.51
10 15 0.11
11 15 0.11
12 6 0.04
13 8 0.06
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (9 bp):
TACATAACT
Found at i:56979478 original size:16 final size:16
Alignment explanation
Indices: 56979457--56979536 Score: 80
Period size: 16 Copynumber: 5.1 Consensus size: 16
56979447 TATTATACAT
56979457 AACTTACATAACTTAC
1 AACTTACATAACTTAC
56979473 AACTTACATAACTTAC
1 AACTTACATAACTTAC
56979489 -A-TTA-AT-A-TTACAC
1 AACTTACATAACTT--AC
*
56979502 ATATTATACATAACTTAC
1 A-ACT-TACATAACTTAC
56979520 AACTTACATAACTTAC
1 AACTTACATAACTTAC
56979536 A
1 A
56979537 TTAATATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
11 2 0.04
12 1 0.02
13 4 0.07
14 3 0.06
15 2 0.04
16 30 0.56
17 4 0.07
18 5 0.09
19 1 0.02
20 2 0.04
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:56979504 original size:47 final size:47
Alignment explanation
Indices: 56979442--56979567 Score: 209
Period size: 47 Copynumber: 2.7 Consensus size: 47
56979432 AACTTAATTA
*
56979442 ATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTACAACTTACATAACTTAC
* *
56979489 ATTAATATTACACAT-ATTATACATAACTTACAACTTACATAACTTAC
1 ATTAATATTATACATAAAT-TACATAACTTACAACTTACATAACTTAC
56979536 ATTAATATTATACATAAATTACATAACTTACA
1 ATTAATATTATACATAAATTACATAACTTACA
56979568 TTAATATTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.03
47 69 0.95
48 2 0.03
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (47 bp):
ATTAATATTATACATAAATTACATAACTTACAACTTACATAACTTAC
Found at i:56979512 original size:31 final size:30
Alignment explanation
Indices: 56979427--56979520 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 30
56979417 ATACATAAAT
56979427 TACATAACTTA-ATT-AATT--A-ATATTA
1 TACATAACTTACATTAAATTACACATATTA
* *
56979452 TACATAACTTACA-TAACTT--ACA-ACT-
1 TACATAACTTACATTAAATTACACATATTA
56979477 TACATAACTTACATTAATATTACACATATTA
1 TACATAACTTACATTAA-ATTACACATATTA
56979508 TACATAACTTACA
1 TACATAACTTACA
56979521 ACTTACATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
25 25 0.45
26 10 0.18
27 3 0.05
29 3 0.05
30 2 0.04
31 13 0.23
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (30 bp):
TACATAACTTACATTAAATTACACATATTA
Found at i:56979558 original size:31 final size:31
Alignment explanation
Indices: 56979406--56979604 Score: 187
Period size: 31 Copynumber: 6.3 Consensus size: 31
56979396 CGTAGAAGCC
56979406 ACATTAATATTATACATAAATTACATAACTT
1 ACATTAATATTATACATAAATTACATAACTT
* *
56979437 AATTAATTAATATTATACATAACTTACATAACTT
1 -A--CATTAATATTATACATAAATTACATAACTT
* * *
56979471 ACAACTTACATAACT-TACATTAATATTACACATATTAT
1 AC-A-TTA-AT-ATTATACA-TAA-ATTACATA-ACT-T
* *
56979509 ACA-T-A-ACT-TAC--AACTTACATAACTT
1 ACATTAATATTATACATAAATTACATAACTT
56979534 ACATTAATATTATACATAAATTACATAACTT
1 ACATTAATATTATACATAAATTACATAACTT
56979565 ACATTAATATTATACATAAATTACATAACTT
1 ACATTAATATTATACATAAATTACATAACTT
56979596 ACATTAATA
1 ACATTAATA
56979605 CGACATAACT
Statistics
Matches: 139, Mismatches: 12, Indels: 33
0.76 0.07 0.18
Matches are distributed among these distances:
25 4 0.03
26 3 0.02
27 7 0.05
28 4 0.03
29 3 0.02
31 59 0.42
32 2 0.01
33 5 0.04
34 34 0.24
35 6 0.04
36 6 0.04
37 3 0.02
38 3 0.02
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (31 bp):
ACATTAATATTATACATAAATTACATAACTT
Found at i:56979643 original size:94 final size:92
Alignment explanation
Indices: 56979545--56979719 Score: 246
Period size: 94 Copynumber: 1.9 Consensus size: 92
56979535 CATTAATATT
56979545 ATACATAAATTACATAACTTACATTAATA-TTATACA-TAAATTACATAACTTACATTAATACGA
1 ATACATAAATTACATAACTT--ATTAATACTTATACATTAAA-TACATAACTTACA-TAATACGA
56979608 CATAACTTATTAATATATTTATGGATAAATG
62 CATAACTTATTAATATATTTATGGATAAATG
* * * *
56979639 ATACATAACTTACATAACTTATTAATACTTTTACATTTTTAATACATAACTTATATAATACGACA
1 ATACATAAATTACATAACTTATTAATACTTATACA--TTAAATACATAACTTACATAATACGACA
56979704 TAACTTATTAATATAT
64 TAACTTATTAATATAT
56979720 ATCATATGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
92 7 0.10
93 6 0.08
94 45 0.62
95 12 0.16
96 3 0.04
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (92 bp):
ATACATAAATTACATAACTTATTAATACTTATACATTAAATACATAACTTACATAATACGACATA
ACTTATTAATATATTTATGGATAAATG
Found at i:56985319 original size:87 final size:87
Alignment explanation
Indices: 56985213--56985410 Score: 258
Period size: 87 Copynumber: 2.3 Consensus size: 87
56985203 ACACAACTTA
* * *
56985213 AAGTGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAAC
1 AAGTAGAGGCAACAGCGAGAGAAGATGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAAC
*
56985276 TTAAAGCAGATGCGGCAATGAGAG
64 TTAAAGCAGATGCGGCAACGAGAG
* * *
56985300 AAGTAGAGGCAGCAGCGAGAGAAGATGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTT
1 AAGTAGAGGCAACAGCGAGAGAAGATGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTT
* *
56985365 AAAGTAGATGCGGCAGCGAGAG
66 AAAGCAGATGCGGCAACGAGAG
*
56985387 AAGTAGAGGCTAA-AGCGAGGGAAG
1 AAGTAGAGGC-AACAGCGAGAGAAG
56985411 TAGAGGCTGC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 91 0.94
88 5 0.05
ACGTcount: A:0.40, C:0.15, G:0.32, T:0.13
Consensus pattern (87 bp):
AAGTAGAGGCAACAGCGAGAGAAGATGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTT
AAAGCAGATGCGGCAACGAGAG
Done.