Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022984.1 Corchorus olitorius cultivar O-4 contig23017, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 109116
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2989 original size:45 final size:42
Alignment explanation
Indices: 2914--3007 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
2904 AGTGCATTAC
* *
2914 CTAA-ATTCTACTCTATCTATAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTATCTATAGATAATTCATCAAAATAAAA
*
2955 CTAATATTCTACTTCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTAC-TCT--ATCTATAGATAATTCATCAAAATAAAA
3000 CTAATATT
1 CTAATATT
3008 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 7 0.15
43 3 0.07
45 32 0.70
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (42 bp):
CTAATATTCTACTCTATCTATAGATAATTCATCAAAATAAAA
Found at i:8785 original size:25 final size:25
Alignment explanation
Indices: 8751--8802 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
8741 GATTCACTTC
8751 TAACTTTGCCTTATAGTATAATCTT
1 TAACTTTGCCTTATAGTATAATCTT
8776 TAACTTTGCCTTATAGTATAATCTT
1 TAACTTTGCCTTATAGTATAATCTT
8801 TA
1 TA
8803 GAGAATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (25 bp):
TAACTTTGCCTTATAGTATAATCTT
Found at i:8990 original size:29 final size:31
Alignment explanation
Indices: 8935--8995 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
8925 AATGCGTTTA
8935 AATAAAAAAAATTAAAATAATTGAAATTATT
1 AATAAAAAAAATTAAAATAATTGAAATTATT
* *
8966 AATAAAAAAATTTTAAA-AATT-AAATTATT
1 AATAAAAAAAATTAAAATAATTGAAATTATT
8995 A
1 A
8996 TATTATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 4 0.14
31 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
AATAAAAAAAATTAAAATAATTGAAATTATT
Found at i:10526 original size:25 final size:26
Alignment explanation
Indices: 10483--10532 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
10473 GATACTGTAC
10483 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
10509 AAATTGAA-TTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
10533 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:30184 original size:121 final size:121
Alignment explanation
Indices: 29968--30266 Score: 438
Period size: 121 Copynumber: 2.5 Consensus size: 121
29958 AGATAATTAT
* * * *
29968 ATTAAATAATCTACCTACCAAAGGTATCTATAGCTA-TCAAATTAACTAGACTTACATCTTAGGA
1 ATTAAATAATCTACCTACCAAAGGTACCTA-A-CTACT-AAATTAACTACACTCACATCTTACGA
* *
30032 GACCACAATTCAAGTACAGTATTACGCATTACACCTAACTACCAGTTGAGTTAATAACC
63 GACCACAATTCAAGTACAATATTACACATTACACCTAACTACCAGTTGAGTTAATAACC
* *
30091 ATTAAATAATCTACTTACCAAAGATACCTAACTACTAAATTAACTACACTCACATCTTACGAGAC
1 ATTAAATAATCTACCTACCAAAGGTACCTAACTACTAAATTAACTACACTCACATCTTACGAGAC
* * * **
30156 CACAATTCAAGTACAATATTGCACATTACACCTAGCTGCCAGTTGAGTTAATAATT
66 CACAATTCAAGTACAATATTACACATTACACCTAACTACCAGTTGAGTTAATAACC
*
30212 ATTAAATAATCTACCTACCAAAGGTACCTAGCTACTAAATTAACTACACTCACAT
1 ATTAAATAATCTACCTACCAAAGGTACCTAACTACTAAATTAACTACACTCACAT
30267 GCACATTACA
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
121 130 0.82
122 2 0.01
123 27 0.17
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (121 bp):
ATTAAATAATCTACCTACCAAAGGTACCTAACTACTAAATTAACTACACTCACATCTTACGAGAC
CACAATTCAAGTACAATATTACACATTACACCTAACTACCAGTTGAGTTAATAACC
Found at i:31103 original size:73 final size:73
Alignment explanation
Indices: 30984--31133 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
30974 AGAAAAACAA
30984 ACTAACTTTATTGAAAATTTTCAAACTTTATTGAAACTCGTACATTCTAAATATAATAATATTGT
1 ACTAACTTTATTGAAAATTTTCAAACTTTATTGAAACTCGTACATTCTAAATATAATAATATTGT
31049 TAGTACCT
66 TAGTACCT
31057 ACTAACTTTATTGAAAATTTTCAAACTTTATTGAAACTCGTACATTCTAAATATAATAATATTGT
1 ACTAACTTTATTGAAAATTTTCAAACTTTATTGAAACTCGTACATTCTAAATATAATAATATTGT
31122 TAGTACCT
66 TAGTACCT
31130 ACTA
1 ACTA
31134 GCTCTCTTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (73 bp):
ACTAACTTTATTGAAAATTTTCAAACTTTATTGAAACTCGTACATTCTAAATATAATAATATTGT
TAGTACCT
Found at i:36647 original size:25 final size:25
Alignment explanation
Indices: 36566--36745 Score: 256
Period size: 25 Copynumber: 7.3 Consensus size: 25
36556 CGGCCATTAC
*
36566 GTGGCCGAATCCCACGACCAAC-AT
1 GTGGCCGAATCTCACGACCAACGAT
* *
36590 GTGGCCGAATCCCACGACC-ACCAT
1 GTGGCCGAATCTCACGACCAACGAT
** * *
36614 GTGATCGAATCTCAAGACCAACTAT
1 GTGGCCGAATCTCACGACCAACGAT
36639 GTGGCCGAATCTCACGACCAACGAT
1 GTGGCCGAATCTCACGACCAACGAT
*
36664 GTGGCCGAGTCTCACGACCAACGAT
1 GTGGCCGAATCTCACGACCAACGAT
*
36689 GTGGCCGAATCTCACGACCAACTAT
1 GTGGCCGAATCTCACGACCAACGAT
36714 GTGGCCGAATCTCACGACCAACGAT
1 GTGGCCGAATCTCACGACCAACGAT
*
36739 ATGGCCG
1 GTGGCCG
36746 TTTGATTTTC
Statistics
Matches: 140, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
23 2 0.01
24 36 0.26
25 102 0.73
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.17
Consensus pattern (25 bp):
GTGGCCGAATCTCACGACCAACGAT
Found at i:37613 original size:2 final size:2
Alignment explanation
Indices: 37606--37645 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
37596 CAACCACCAC
* * *
37606 AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37646 TAGAGTACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37628 original size:14 final size:14
Alignment explanation
Indices: 37609--37645 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37599 CCACCACATA
*
37609 TATATATATGTATG
1 TATATATATATATG
37623 TATATATATATATG
1 TATATATATATATG
37637 TATATATAT
1 TATATATAT
37646 TAGAGTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (14 bp):
TATATATATATATG
Found at i:42144 original size:37 final size:37
Alignment explanation
Indices: 42101--42175 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
42091 AGGATTGTTA
*
42101 AGACAAGAGTCTTAAAAAGAGTAGACAAGAGTCTAAG
1 AGACAAGAGTCTTAAAAAGAATAGACAAGAGTCTAAG
*
42138 AGACAAGAGTCTTAAAGAGAATAGACAAGAGTCTAAG
1 AGACAAGAGTCTTAAAAAGAATAGACAAGAGTCTAAG
42175 A
1 A
42176 AAACAAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.11, G:0.24, T:0.16
Consensus pattern (37 bp):
AGACAAGAGTCTTAAAAAGAATAGACAAGAGTCTAAG
Found at i:42775 original size:25 final size:25
Alignment explanation
Indices: 42747--42927 Score: 238
Period size: 25 Copynumber: 7.3 Consensus size: 25
42737 CGGCCATTAC
*
42747 GTGGCCGAATCCCACGACCAACTAT
1 GTGGCCGAATCTCACGACCAACTAT
* *
42772 GTGGCCGAATCCCACGACC-ACCAT
1 GTGGCCGAATCTCACGACCAACTAT
** *
42796 GTGATCGAATCTCAAGACCAACTAT
1 GTGGCCGAATCTCACGACCAACTAT
* **
42821 GTGGTCGTTTCTCACGACCAACTAT
1 GTGGCCGAATCTCACGACCAACTAT
*
42846 GTGGCCGAATCTCACGACCAACGAT
1 GTGGCCGAATCTCACGACCAACTAT
*
42871 GTGGCCGAATCTCACGACCAACGAT
1 GTGGCCGAATCTCACGACCAACTAT
* *
42896 GTGGCCAAATCTCACGATCAACTAT
1 GTGGCCGAATCTCACGACCAACTAT
42921 GTGGCCG
1 GTGGCCG
42928 TTTGATTTTC
Statistics
Matches: 137, Mismatches: 18, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
24 19 0.14
25 118 0.86
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (25 bp):
GTGGCCGAATCTCACGACCAACTAT
Found at i:46635 original size:138 final size:134
Alignment explanation
Indices: 46407--46661 Score: 397
Period size: 138 Copynumber: 1.9 Consensus size: 134
46397 ACTAGTTACT
46407 AGTTTAACTACTCCAACACCTACCATTCCATTCTATTGGAATTAACAAGTGTACTATAAATAAAT
1 AGTTTAACTACTCCAACACCTACCATTCCATTCTATTGGAATTAACAAGTGTACTATAAATAAAT
46472 ATACAAAATTTGTGCATTATTCAATTTCATTTCCATCATCATTTCATTGCATTTATTATTACTAG
66 ATACAAAATTTGTGCATTATTC-A----A-TTCCATCATCATTTCATTGCATTTATTATTACTAG
46537 TTACTACTCC
125 TTACTACTCC
* * *
46547 AGTTTAACTACTCCAACACCTACCATTCTA-T-TGTTGGAATTAACAAGTGTGCTATAAATAAAT
1 AGTTTAACTACTCCAACACCTACCATTCCATTCTATTGGAATTAACAAGTGTACTATAAATAAAT
* *
46610 ATACAAATTTTGTGCATTGTTCAATTCCATCATCATTTCATTGCATTTATTA
66 ATACAAAATTTGTGCATTATTCAATTCCATCATCATTTCATTGCATTTATTA
46662 GAAATTGCAT
Statistics
Matches: 110, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
132 28 0.25
133 1 0.01
137 1 0.01
138 50 0.45
139 1 0.01
140 29 0.26
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (134 bp):
AGTTTAACTACTCCAACACCTACCATTCCATTCTATTGGAATTAACAAGTGTACTATAAATAAAT
ATACAAAATTTGTGCATTATTCAATTCCATCATCATTTCATTGCATTTATTATTACTAGTTACTA
CTCC
Found at i:46754 original size:15 final size:16
Alignment explanation
Indices: 46719--46757 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
46709 AAGAGAGATG
46719 CCGCCACCGGGATGGGGA
1 CCGCCACCGGGA--GGGA
46737 CCGCCACCGGGA-GGA
1 CCGCCACCGGGAGGGA
46752 CCGCCA
1 CCGCCA
46758 GGGCCTCCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
18 12 0.57
ACGTcount: A:0.18, C:0.41, G:0.38, T:0.03
Consensus pattern (16 bp):
CCGCCACCGGGAGGGA
Found at i:57113 original size:19 final size:22
Alignment explanation
Indices: 57084--57132 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
57074 CATGTTTTCT
*
57084 TAATA-ATATATAAATAT-TAC
1 TAATATATATATATATATATAC
57104 TAATATATATATATATATATAC
1 TAATATATATATATATATATAC
57126 T-ATATAT
1 TAATATAT
57133 TATTTTTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 17 0.65
22 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATATATATATATATATAC
Found at i:58374 original size:14 final size:13
Alignment explanation
Indices: 58355--58393 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
58345 AAATTAAAAA
58355 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
58368 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
58382 ATTTAAAAAATT
1 ATTTAAAAAATT
58394 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:58616 original size:122 final size:127
Alignment explanation
Indices: 58379--58632 Score: 401
Period size: 122 Copynumber: 2.0 Consensus size: 127
58369 ATTTAAGAAA
58379 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAAT---A
* *
58444 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
58509 G
127 G
*
58510 TATATTT-AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATACAG
*
58572 TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
58632 T
1 T
58633 TTAAACAATG
Statistics
Matches: 119, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
122 55 0.46
123 2 0.02
124 2 0.02
126 1 0.01
130 52 0.44
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:90630 original size:5 final size:5
Alignment explanation
Indices: 90620--90646 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
90610 CGTTAGGTCA
90620 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
90647 TAATAAAAAG
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:90989 original size:28 final size:28
Alignment explanation
Indices: 90949--91009 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
90939 ACAACCTCAA
*
90949 TTGGCATGTTAGGCCTTTATTTCAGCCC
1 TTGGTATGTTAGGCCTTTATTTCAGCCC
*
90977 TTGGTATGTTAGGCCTTTATTTGAGCCC
1 TTGGTATGTTAGGCCTTTATTTCAGCCC
91005 TTGGT
1 TTGGT
91010 CTTATCTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.43
Consensus pattern (28 bp):
TTGGTATGTTAGGCCTTTATTTCAGCCC
Found at i:100534 original size:45 final size:42
Alignment explanation
Indices: 100485--100578 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
100475 AGCAACAATT
*
100485 AATATTAGCTTTATTTTGATGAATTATCTAGAGATAGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT---GGAGTAG
* *
100530 AATATCAACTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
100572 AAT-TTAG
1 AATATTAG
100579 ATAATGCACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.05
42 10 0.23
45 32 0.73
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:100891 original size:103 final size:103
Alignment explanation
Indices: 100778--100963 Score: 372
Period size: 103 Copynumber: 1.8 Consensus size: 103
100768 GCCCTGCTTG
100778 TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATACA
1 TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATACA
100843 AAATGCAATGAACTATTGAATAATTCTATTATATAATA
66 AAATGCAATGAACTATTGAATAATTCTATTATATAATA
100881 TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATACA
1 TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATACA
100946 AAATGCAATGAACTATTG
66 AAATGCAATGAACTATTG
100964 GACCTATTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (103 bp):
TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATACA
AAATGCAATGAACTATTGAATAATTCTATTATATAATA
Found at i:100992 original size:53 final size:53
Alignment explanation
Indices: 100907--101018 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
100897 TGTTTATTCA
*
100907 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGGACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
100960 ATTGGACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGGACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
101013 ATTGGA
1 ATTGGA
101019 TTTAGAGAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.23
Consensus pattern (53 bp):
ATTGGACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:105048 original size:27 final size:27
Alignment explanation
Indices: 104989--105050 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
104979 AAAAATACAC
* * *
104989 AAAATTATATTTTAATAGTGGCATTATT
1 AAAA-TATTTTTTAATAATGGCAATATT
105017 AAAATATTTTTTAATAATGGCAAT-TT
1 AAAATATTTTTTAATAATGGCAATATT
105043 AGAAATAT
1 A-AAATAT
105051 ATCTATACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.77
28 4 0.13
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (27 bp):
AAAATATTTTTTAATAATGGCAATATT
Found at i:107801 original size:22 final size:21
Alignment explanation
Indices: 107754--107834 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 21
107744 CTTATGGAGT
* * *
107754 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATAGGTGA
*
107775 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATA-GGTGA
*
107797 TTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTCATA-GGTGA
*
107819 TTATCGAAATTTCATA
1 TTATCAAAATTTCATA
107835 AAAAATTCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 14 0.28
22 36 0.72
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGA
Found at i:107801 original size:43 final size:44
Alignment explanation
Indices: 107734--107834 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
107724 TAGTTAGGTC
* * * * *
107734 ATCAAAGTTTCTTATGGAGTTTATCACAATTTTATA-GGTAATT
1 ATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAATT
* *
107777 ATCAAAATTTCATATGGTGGTTATCAAAATTTAATAGGGTGATT
1 ATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAATT
*
107821 ATCGAAATTTCATA
1 ATCAAAATTTCATA
107835 AAAAATTCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 30 0.61
44 19 0.39
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.41
Consensus pattern (44 bp):
ATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAATT
Done.