Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008807.1 Corchorus capsularis cultivar CVL-1 contig08828, 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: 15821
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:33 original size:2 final size:2
Alignment explanation
Indices: 26--57 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16 CTCTCATTCC
26 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58 CTTTATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1052 original size:2 final size:2
Alignment explanation
Indices: 1045--1076 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1035 AATTATCTTG
1045 AT AT AT AT AT A- 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 AT AT AT A
1077 CCAAAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3991 original size:21 final size:19
Alignment explanation
Indices: 3947--4000 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 19
3937 TATACTAATA
3947 AAAAATAATAAAT-ATATT
1 AAAAATAATAAATAATATT
**
3965 TTAAATAATAAATAATGAGTT
1 AAAAATAATAAATAAT-A-TT
3986 AAAAATAAATAAATA
1 AAAAAT-AATAAATA
4001 TTATATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 1 0.04
21 6 0.21
22 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAATAATAAATAATATT
Found at i:7105 original size:2 final size:2
Alignment explanation
Indices: 7100--7135 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7090 TTTTTGTTAC
7100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7136 GGTGATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7443 original size:21 final size:21
Alignment explanation
Indices: 7419--7461 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7409 ACTGTACAGA
7419 GTCATTGTTGCTTTAGAATCT
1 GTCATTGTTGCTTTAGAATCT
7440 GTCATTGTTGCTTTAGAATCT
1 GTCATTGTTGCTTTAGAATCT
7461 G
1 G
7462 AGGTTGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (21 bp):
GTCATTGTTGCTTTAGAATCT
Found at i:7831 original size:2 final size:2
Alignment explanation
Indices: 7824--7850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7814 TGTTTCTTAT
7824 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7851 GCATTATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9317 original size:23 final size:24
Alignment explanation
Indices: 9272--9321 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
9262 CACGAAACAT
*
9272 AAACAATACACTATTAAAATTTAG
1 AAACAATACACTACTAAAATTTAG
* *
9296 AAACAATGCA-TACTAAAGTTTAG
1 AAACAATACACTACTAAAATTTAG
9319 AAA
1 AAA
9322 GTTTGCCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (24 bp):
AAACAATACACTACTAAAATTTAG
Found at i:13691 original size:21 final size:20
Alignment explanation
Indices: 13662--13702 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13652 TAATAATCAT
*
13662 ATTATTTATACATAAAAATAA
1 ATTAATTATA-ATAAAAATAA
13683 ATTAATTATAATAAAAATAA
1 ATTAATTATAATAAAAATAA
13703 TATATTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAATTATAATAAAAATAA
Found at i:13766 original size:36 final size:35
Alignment explanation
Indices: 13698--13766 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
13688 TTATAATAAA
* *
13698 AATAATATATTTAGATAATACTTGTAAAATTAACT
1 AATAATATAATTAGATAATACATGTAAAATTAACT
*
13733 AATAATAATAATTAG-TATATACATGTAATATTAA
1 AATAAT-ATAATTAGATA-ATACATGTAAAATTAA
13767 TTTATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 8 0.28
36 21 0.72
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (35 bp):
AATAATATAATTAGATAATACATGTAAAATTAACT
Found at i:15302 original size:12 final size:12
Alignment explanation
Indices: 15273--15315 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
15263 TCATCCTCAT
15273 AAGATGAGGATG
1 AAGATGAGGATG
** *
15285 GGGATGGGGATG
1 AAGATGAGGATG
*
15297 AAGATGAAGATG
1 AAGATGAGGATG
15309 AAGATGA
1 AAGATGA
15316 AAAAACAGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
AAGATGAGGATG
Found at i:15603 original size:139 final size:139
Alignment explanation
Indices: 15435--15819 Score: 743
Period size: 139 Copynumber: 2.7 Consensus size: 139
15425 AAATGTAGCC
15435 GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTCTGCACACTA
1 GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTCTGCACACTA
15500 TCCAAGGCATGTCAGAAAATCAAACACAACATTCAAAAACTTTTCAGAAAATCTAATCCTATTTC
66 TCCAAGGCATGTCAGAAAATCAAACACAACATTCAAAAACTTTTCAGAAAATCTAATCCTATTTC
15565 ACTCCAACG
131 ACTCCAACG
15574 GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTCTGCACACTA
1 GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTCTGCACACTA
15639 TCCAAGGCATGTCAGAAAATCAAACACAACATTCAAAAAACTTTTCAGAAAATCTAATCCTATTT
66 TCCAAGGCATGTCAGAAAATCAAACACAACATTC-AAAAACTTTTCAGAAAATCTAATCCTATTT
15704 CACTCCAACG
130 CACTCCAACG
15714 GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTCGTGCACACT
1 GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTC-TGCACACT
15779 ATCCAAAGGCATGTCAGAAAATCAAACACAACATTCAAAAA
65 ATCC-AAGGCATGTCAGAAAATCAAACACAACATTCAAAAA
15820 AC
Statistics
Matches: 243, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
139 99 0.41
140 96 0.40
141 17 0.07
142 31 0.13
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (139 bp):
GTTGGATTTAAACGTTCATATTCAAATGTGACCGTTGATTAAAACCTTATCTCTTCTGCACACTA
TCCAAGGCATGTCAGAAAATCAAACACAACATTCAAAAACTTTTCAGAAAATCTAATCCTATTTC
ACTCCAACG
Done.