Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014570.1 Corchorus capsularis cultivar CVL-1 contig14591, 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: 96995
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:737 original size:17 final size:17
Alignment explanation
Indices: 701--738 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
691 GTATTATTAT
*
701 TATATATATAATATATA
1 TATATATATAATATACA
*
718 TATATATATAATCTACA
1 TATATATATAATATACA
735 TATA
1 TATA
739 ATTTGAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATATATAATATACA
Found at i:1896 original size:7 final size:7
Alignment explanation
Indices: 1878--1921 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1868 TCTAGATGGG
1878 TTGGAC-
1 TTGGACA
1884 TTGGACA
1 TTGGACA
1891 TTGGACA
1 TTGGACA
*
1898 TTGCACA
1 TTGGACA
1905 TTGGACA
1 TTGGACA
1912 TTGGACA
1 TTGGACA
1919 TTG
1 TTG
1922 TTGAGTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (7 bp):
TTGGACA
Found at i:6584 original size:12 final size:12
Alignment explanation
Indices: 6567--6591 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6557 ATGACGGCGA
6567 TAAGGGAACACC
1 TAAGGGAACACC
6579 TAAGGGAACACC
1 TAAGGGAACACC
6591 T
1 T
6592 GCGATCGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (12 bp):
TAAGGGAACACC
Found at i:7053 original size:6 final size:6
Alignment explanation
Indices: 7042--7076 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
7032 TCTGTGCTTC
7042 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
7077 GCCTTATTTT
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
TCTCTT
Found at i:11686 original size:14 final size:14
Alignment explanation
Indices: 11667--11693 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11657 TACCACTCCT
11667 TGTAACTTGTAACC
1 TGTAACTTGTAACC
11681 TGTAACTTGTAAC
1 TGTAACTTGTAAC
11694 ATTACCGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
TGTAACTTGTAACC
Found at i:22773 original size:13 final size:13
Alignment explanation
Indices: 22755--22779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22745 TAATCATCTC
22755 ATATATATACATA
1 ATATATATACATA
22768 ATATATATACAT
1 ATATATATACAT
22780 GCATGATCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATATACATA
Found at i:36398 original size:31 final size:31
Alignment explanation
Indices: 36355--36416 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
36345 TTTGTGCGCA
* * *
36355 TGGCATGTCACGTGTCATTTTTTGGTACATG
1 TGGCATGTCACGTATCACTTTTTGATACATG
*
36386 TGGCTTGTCACGTATCACTTTTTGATACATG
1 TGGCATGTCACGTATCACTTTTTGATACATG
36417 ACATGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (31 bp):
TGGCATGTCACGTATCACTTTTTGATACATG
Found at i:37067 original size:2 final size:2
Alignment explanation
Indices: 37060--37085 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37050 CGGAGGGTTA
37060 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
37086 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52358 original size:6 final size:6
Alignment explanation
Indices: 52347--52371 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52337 TGATAAATCA
52347 GAATAT GAATAT GAATAT GAATAT G
1 GAATAT GAATAT GAATAT GAATAT G
52372 CCTGCCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (6 bp):
GAATAT
Found at i:61314 original size:27 final size:28
Alignment explanation
Indices: 61275--61340 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
61265 TAAGCTTTAA
*
61275 AAGGCTTTTAAG-ATCTGACCC-AACAG
1 AAGGCTTTTAAGAATCTGACCCAAAAAG
* *
61301 ATAGGCTTTTAAGAATGTGGCCCAAAAAG
1 A-AGGCTTTTAAGAATCTGACCCAAAAAG
61330 AAGGCTTTTAA
1 AAGGCTTTTAA
61341 TAGGGCATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.03
27 11 0.32
28 17 0.50
29 5 0.15
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (28 bp):
AAGGCTTTTAAGAATCTGACCCAAAAAG
Found at i:82791 original size:21 final size:21
Alignment explanation
Indices: 82753--82879 Score: 87
Period size: 21 Copynumber: 6.0 Consensus size: 21
82743 TTCTCTCCTA
* * *
82753 CATCATCCCCAGGTTACAGCC
1 CATCATCTCCTGGATACAGCC
* *
82774 CATCTTCTCCTGGATACAGTC
1 CATCATCTCCTGGATACAGCC
* * *
82795 CATCATCCCCTGGCTACAGTC
1 CATCATCTCCTGGATACAGCC
* * * * *
82816 CAACCTCGCCTGGTTACAGTC
1 CATCATCTCCTGGATACAGCC
*
82837 C-TACATCTCCTGGATATAGCCC
1 CAT-CATCTCCTGGATACAG-CC
*
82859 CA-CATCTCCTGGGTACAGCC
1 CATCATCTCCTGGATACAGCC
82879 C
1 C
82880 CACATCACCT
Statistics
Matches: 83, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
20 3 0.04
21 78 0.94
22 2 0.02
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.24
Consensus pattern (21 bp):
CATCATCTCCTGGATACAGCC
Found at i:82813 original size:42 final size:41
Alignment explanation
Indices: 82753--82876 Score: 106
Period size: 42 Copynumber: 3.0 Consensus size: 41
82743 TTCTCTCCTA
* * *
82753 CATCATCCCCAGGTTACAGCCCATCTTCTCCTGGATACAGTC
1 CATCATCCCCTGGATACAGCCCA-CATCTCCTGGATACAGTC
* * * * *
82795 CATCATCCCCTGGCTACAGTCCAACCTCGCCTGGTTACAGTC
1 CATCATCCCCTGGATACAG-CCCACATCTCCTGGATACAGTC
* * *
82837 C-TACATCTCCTGGATATAGCCCCACATCTCCTGGGTACAG
1 CAT-CATCCCCTGGATACAG-CCCACATCTCCTGGATACAG
82877 CCCCACATCA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.94
43 3 0.05
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (41 bp):
CATCATCCCCTGGATACAGCCCACATCTCCTGGATACAGTC
Found at i:82880 original size:21 final size:21
Alignment explanation
Indices: 82779--82885 Score: 90
Period size: 21 Copynumber: 5.1 Consensus size: 21
82769 CAGCCCATCT
*
82779 TCTCCTGGATACAG-TCCATCA
1 TCTCCTGGATACAGCCCCA-CA
* * * * *
82800 TCCCCTGGCTACAGTCCAACC
1 TCTCCTGGATACAGCCCCACA
* * * *
82821 TCGCCTGGTTACAGTCCTACA
1 TCTCCTGGATACAGCCCCACA
*
82842 TCTCCTGGATATAGCCCCACA
1 TCTCCTGGATACAGCCCCACA
*
82863 TCTCCTGGGTACAGCCCCACA
1 TCTCCTGGATACAGCCCCACA
82884 TC
1 TC
82886 ACCTACTTAC
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
21 67 0.97
22 2 0.03
ACGTcount: A:0.21, C:0.39, G:0.16, T:0.24
Consensus pattern (21 bp):
TCTCCTGGATACAGCCCCACA
Found at i:82896 original size:21 final size:21
Alignment explanation
Indices: 82854--82897 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
82844 TCCTGGATAT
* **
82854 AGCCCCACATCTCCTGGGTAC
1 AGCCCCACATCACCTACGTAC
*
82875 AGCCCCACATCACCTACTTAC
1 AGCCCCACATCACCTACGTAC
82896 AG
1 AG
82898 TCCAAGTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (21 bp):
AGCCCCACATCACCTACGTAC
Found at i:83001 original size:21 final size:21
Alignment explanation
Indices: 82971--83044 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
82961 TCCGACCTCT
* *
82971 CCAAGCTACAGCCCTACATCG
1 CCAAGTTACAGCCCTACATCC
82992 CCAAGTTACAGCCCTACATCC
1 CCAAGTTACAGCCCTACATCC
*
83013 CCAAGTTACAGTCCC-ACTTCC
1 CCAAGTTACAG-CCCTACATCC
83034 CCAAGTTACAG
1 CCAAGTTACAG
83045 TCCCACCTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 46 0.94
22 3 0.06
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.19
Consensus pattern (21 bp):
CCAAGTTACAGCCCTACATCC
Found at i:83045 original size:21 final size:21
Alignment explanation
Indices: 82992--83092 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 21
82982 CCCTACATCG
*
82992 CCAAGTTACAG-CCCTACATCC
1 CCAAGTTACAGTCCC-ACTTCC
83013 CCAAGTTACAGTCCCACTTCC
1 CCAAGTTACAGTCCCACTTCC
* *
83034 CCAAGTTACAGTCCCACCTCT
1 CCAAGTTACAGTCCCACTTCC
* * * * *
83055 CCGAGCTATAGTCCAACTTCA
1 CCAAGTTACAGTCCCACTTCC
* *
83076 CCTAGTTACAGCCCCAC
1 CCAAGTTACAGTCCCAC
83093 GTCACCTGTA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
21 62 0.95
22 3 0.05
ACGTcount: A:0.26, C:0.42, G:0.11, T:0.22
Consensus pattern (21 bp):
CCAAGTTACAGTCCCACTTCC
Found at i:83068 original size:42 final size:41
Alignment explanation
Indices: 82965--83089 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
82955 TTATTCTCCG
* *
82965 ACCTCTCCAAGCTACAG-CCCTACATCGCCAAGTTACAGCCC
1 ACCTCTCCAAGCTACAGTCCC-ACTTCACCAAGTTACAGCCC
* * * *
83006 TACATCCCCAAGTTACAGTCCCACTTCCCCAAGTTACAGTCCC
1 -ACCTCTCCAAGCTACAGTCCCACTTCACCAAGTTACAG-CCC
* * * *
83049 ACCTCTCCGAGCTATAGTCCAACTTCACCTAGTTACAGCCC
1 ACCTCTCCAAGCTACAGTCCCACTTCACCAAGTTACAGCCC
83090 CACGTCACCT
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.04
42 59 0.87
43 6 0.09
ACGTcount: A:0.26, C:0.42, G:0.11, T:0.22
Consensus pattern (41 bp):
ACCTCTCCAAGCTACAGTCCCACTTCACCAAGTTACAGCCC
Found at i:83099 original size:21 final size:21
Alignment explanation
Indices: 82971--83098 Score: 85
Period size: 21 Copynumber: 6.1 Consensus size: 21
82961 TCCGACCTCT
* * *
82971 CCAAGCTACAGCCCTACATCG
1 CCAAGTTACAGCCCCACATCA
* *
82992 CCAAGTTACAGCCCTACATCC
1 CCAAGTTACAGCCCCACATCA
* * *
83013 CCAAGTTACAGTCCCACTTCC
1 CCAAGTTACAGCCCCACATCA
* * *
83034 CCAAGTTACAGTCCCACCTCT
1 CCAAGTTACAGCCCCACATCA
* * * * * *
83055 CCGAGCTATAGTCCAACTTCA
1 CCAAGTTACAGCCCCACATCA
* *
83076 CCTAGTTACAGCCCCACGTCA
1 CCAAGTTACAGCCCCACATCA
83097 CC
1 CC
83099 TGTATATAGC
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.26, C:0.42, G:0.12, T:0.20
Consensus pattern (21 bp):
CCAAGTTACAGCCCCACATCA
Found at i:83107 original size:42 final size:42
Alignment explanation
Indices: 83061--83176 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
83051 CTCTCCGAGC
* * *
83061 TATAGTCCAACTTCACCTAG-TTACAGCCCCACGTCACCTGTA
1 TATAGTCCAACTTCACCT-GCATACAGCCCAACGTCACCTGCA
* * *
83103 TATAGCCCAACTTCACCTGCATACAGCCCAACTTCACCTGCC
1 TATAGTCCAACTTCACCTGCATACAGCCCAACGTCACCTGCA
* *
83145 TATAGTCCCACTTCTCCAT-CATACAGCCCAAC
1 TATAGTCCAACTTCACC-TGCATACAGCCCAAC
83177 ATCCCCATCA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (42 bp):
TATAGTCCAACTTCACCTGCATACAGCCCAACGTCACCTGCA
Found at i:83109 original size:21 final size:21
Alignment explanation
Indices: 83067--83176 Score: 100
Period size: 21 Copynumber: 5.2 Consensus size: 21
83057 GAGCTATAGT
*
83067 CCAACTTCACCTAG-TTACAGC
1 CCAACTTCACCT-GCATACAGC
* * * *
83088 CCCACGTCACCTGTATATAGC
1 CCAACTTCACCTGCATACAGC
83109 CCAACTTCACCTGCATACAGC
1 CCAACTTCACCTGCATACAGC
* *
83130 CCAACTTCACCTGCCTATAGTC
1 CCAACTTCACCTGCATACAG-C
*
83152 CC-ACTTCTCCAT-CATACAGC
1 CCAACTTCACC-TGCATACAGC
83172 CCAAC
1 CCAAC
83177 ATCCCCATCA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.06
21 64 0.89
22 4 0.06
ACGTcount: A:0.26, C:0.42, G:0.09, T:0.23
Consensus pattern (21 bp):
CCAACTTCACCTGCATACAGC
Found at i:83189 original size:63 final size:62
Alignment explanation
Indices: 83122--83288 Score: 163
Period size: 63 Copynumber: 2.6 Consensus size: 62
83112 ACTTCACCTG
* *
83122 CATACAGCCCAACTTCACCTGCCTATAGTCCCACTTCTCCATCATACAGCCCAACATCCCCAT
1 CATACAGTCCAACTTCTCCTGCCTATAG-CCCACTTCTCCATCATACAGCCCAACATCCCCAT
* * * * * * * * * * * *
83185 CATACAGTCCAACATCTCCTTCTTACAGCCCGACCTCACCCTCCTATAGCCCTACGTCTCCAT
1 CATACAGTCCAACTTCTCCTGCCTATAGCCC-ACTTCTCCATCATACAGCCCAACATCCCCAT
* *
83248 CATACAGTCCTACTTCTCCAGCCTATAGCCCCACTTCTCCA
1 CATACAGTCCAACTTCTCCTGCCTATAG-CCCACTTCTCCA
83289 GGGTACAGTC
Statistics
Matches: 79, Mismatches: 23, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
62 3 0.04
63 73 0.92
64 3 0.04
ACGTcount: A:0.24, C:0.44, G:0.07, T:0.25
Consensus pattern (62 bp):
CATACAGTCCAACTTCTCCTGCCTATAGCCCACTTCTCCATCATACAGCCCAACATCCCCAT
Found at i:83194 original size:42 final size:41
Alignment explanation
Indices: 83122--83254 Score: 124
Period size: 42 Copynumber: 3.2 Consensus size: 41
83112 ACTTCACCTG
* * *
83122 CATACAGCCCAACTTCACCTGCCTATAGTCCCACTTCTCCAT
1 CATACAGCCCAACATCCCCT-CCTATAGTCCCACATCTCCAT
* * * *
83164 CATACAGCCCAACATCCCCATCATACAGTCCAACATCTCCTT
1 CATACAGCCCAACATCCCC-TCCTATAGTCCCACATCTCCAT
* * * *
83206 CTTACAGCCCGACCTCACCCTCCTATAG-CCCTACGTCTCCAT
1 CATACAGCCCAACATC-CCCTCCTATAGTCCC-ACATCTCCAT
83248 CATACAG
1 CATACAG
83255 TCCTACTTCT
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.03
42 66 0.92
43 4 0.06
ACGTcount: A:0.26, C:0.44, G:0.08, T:0.23
Consensus pattern (41 bp):
CATACAGCCCAACATCCCCTCCTATAGTCCCACATCTCCAT
Found at i:83267 original size:21 final size:21
Alignment explanation
Indices: 83157--83254 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 21
83147 TAGTCCCACT
83157 TCTCCATCATACAGCCCAACA
1 TCTCCATCATACAGCCCAACA
* *
83178 TCCCCATCATACAGTCCAACA
1 TCTCCATCATACAGCCCAACA
* * * *
83199 TCTCCTTCTTACAGCCCGACC
1 TCTCCATCATACAGCCCAACA
* * * * * *
83220 TCACCCTCCTATAGCCCTACG
1 TCTCCATCATACAGCCCAACA
83241 TCTCCATCATACAG
1 TCTCCATCATACAG
83255 TCCTACTTCT
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.26, C:0.44, G:0.07, T:0.23
Consensus pattern (21 bp):
TCTCCATCATACAGCCCAACA
Found at i:83283 original size:21 final size:21
Alignment explanation
Indices: 83227--83289 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
83217 ACCTCACCCT
* *
83227 CCTATAGCCCTACGTCTCCAT
1 CCTATAGCCCTACTTCTCCAG
* * *
83248 CATACAGTCCTACTTCTCCAG
1 CCTATAGCCCTACTTCTCCAG
*
83269 CCTATAGCCCCACTTCTCCAG
1 CCTATAGCCCTACTTCTCCAG
83290 GGTACAGTCC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.43, G:0.10, T:0.27
Consensus pattern (21 bp):
CCTATAGCCCTACTTCTCCAG
Found at i:83331 original size:21 final size:21
Alignment explanation
Indices: 83307--83384 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
83297 TCCAACCTCA
83307 CCAAGTTATAGTCCGACATCG
1 CCAAGTTATAGTCCGACATCG
* * * *
83328 CCAAGCTATAGTCCTACCTCT
1 CCAAGTTATAGTCCGACATCG
* *
83349 CCAAGTTACAATCC-ACAGTCTG
1 CCAAGTTATAGTCCGACA-TC-G
83371 CCAAG-TATAGTCCG
1 CCAAGTTATAGTCCG
83385 TCTCTTGCAT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.05
21 36 0.84
22 5 0.12
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.24
Consensus pattern (21 bp):
CCAAGTTATAGTCCGACATCG
Found at i:83347 original size:42 final size:42
Alignment explanation
Indices: 83295--83383 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
83285 TCCAGGGTAC
* *
83295 AGTCCAACCTCACCAAGTTATAGTCCGACA-TC-GCCAAGCTAT
1 AGTCCAACCTCACCAAGTTACAATCC-ACAGTCTGCCAAG-TAT
* *
83337 AGTCCTACCTCTCCAAGTTACAATCCACAGTCTGCCAAGTAT
1 AGTCCAACCTCACCAAGTTACAATCCACAGTCTGCCAAGTAT
83379 AGTCC
1 AGTCC
83384 GTCTCTTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 32 0.78
43 6 0.15
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.24
Consensus pattern (42 bp):
AGTCCAACCTCACCAAGTTACAATCCACAGTCTGCCAAGTAT
Found at i:83656 original size:21 final size:21
Alignment explanation
Indices: 83623--83663 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
83613 TAATTGCAGC
83623 CCAACATCGCCATCATATTCA
1 CCAACATCGCCATCATATTCA
* * *
83644 CCAACTTCTCCATCTTATTC
1 CCAACATCGCCATCATATTC
83664 CCCTTCCAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.39, G:0.02, T:0.32
Consensus pattern (21 bp):
CCAACATCGCCATCATATTCA
Found at i:87134 original size:6 final size:6
Alignment explanation
Indices: 87123--87150 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
87113 TGATCATCAC
87123 TTCATT TTCATT TTCATT TTCATT TTCA
1 TTCATT TTCATT TTCATT TTCATT TTCA
87151 ACCACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCATT
Done.