Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010307.1 Corchorus capsularis cultivar CVL-1 contig10328, 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: 17945
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:4698 original size:41 final size:41
Alignment explanation
Indices: 4652--4733 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
4642 ACTTGTCCCT
*
4652 CCTAATAATTAAGGAAATAAATTAAATCCAGATTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
* * * *
4693 CCTAATAATTAAGGTAAGAATTTAAATTCAGGTTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
4734 TAGTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
Found at i:6257 original size:10 final size:10
Alignment explanation
Indices: 6242--6273 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
6232 CATATCTCGG
6242 TCGACTCAAC
1 TCGACTCAAC
*
6252 TCGACTCGAC
1 TCGACTCAAC
6262 TCGACTCAAC
1 TCGACTCAAC
6272 TC
1 TC
6274 ACCTCCTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (10 bp):
TCGACTCAAC
Found at i:12929 original size:34 final size:34
Alignment explanation
Indices: 12890--13019 Score: 153
Period size: 34 Copynumber: 4.0 Consensus size: 34
12880 TCTCACACTT
*
12890 TGTTCTTTTTCTGGGTATTTGATTTCTTGATTTC
1 TGTTCTTGTTCTGGGTATTTGATTTCTTGATTTC
*
12924 TGTTCTTGTTCTGGGTTTTTGATTTCTTGA--T-
1 TGTTCTTGTTCTGGGTATTTGATTTCTTGATTTC
** ***
12955 T-TTCCGGGAAT-GGTATTTGATTTCTTGATTTC
1 TGTTCTTGTTCTGGGTATTTGATTTCTTGATTTC
*
12987 TGTTCTTGTTCTGGGTTTTTGATTTCTTGATTT
1 TGTTCTTGTTCTGGGTATTTGATTTCTTGATTT
13020 TCCGGGAATG
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
29 16 0.21
30 5 0.06
31 2 0.03
32 2 0.03
33 5 0.06
34 47 0.61
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (34 bp):
TGTTCTTGTTCTGGGTATTTGATTTCTTGATTTC
Found at i:12976 original size:63 final size:64
Alignment explanation
Indices: 12901--13046 Score: 276
Period size: 63 Copynumber: 2.3 Consensus size: 64
12891 GTTCTTTTTC
12901 TGGGTATTTGATTTCTTGATTTCTGTTCTTGTTCTGGGTTTTTGATTTCTTGATTTTCCGGGAA
1 TGGGTATTTGATTTCTTGATTTCTGTTCTTGTTCTGGGTTTTTGATTTCTTGATTTTCCGGGAA
12965 T-GGTATTTGATTTCTTGATTTCTGTTCTTGTTCTGGGTTTTTGATTTCTTGATTTTCCGGGAA
1 TGGGTATTTGATTTCTTGATTTCTGTTCTTGTTCTGGGTTTTTGATTTCTTGATTTTCCGGGAA
*
13028 TGGGTAGTTGATTTCTTGA
1 TGGGTATTTGATTTCTTGA
13047 CGGAGACCTC
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
63 63 0.79
64 17 0.21
ACGTcount: A:0.12, C:0.10, G:0.24, T:0.54
Consensus pattern (64 bp):
TGGGTATTTGATTTCTTGATTTCTGTTCTTGTTCTGGGTTTTTGATTTCTTGATTTTCCGGGAA
Found at i:13525 original size:24 final size:25
Alignment explanation
Indices: 13497--13555 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
13487 AAATTTTTGC
13497 TTTTGTTTAAAAA-TTTTTTATGAG
1 TTTTGTTTAAAAATTTTTTTATGAG
13521 TTTTGTTTAAAAATTTTTTTATGAG
1 TTTTGTTTAAAAATTTTTTTATGAG
13546 TTTTGTTTAA
1 TTTTGTTTAA
13556 GAAGAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (25 bp):
TTTTGTTTAAAAATTTTTTTATGAG
Found at i:13529 original size:13 final size:13
Alignment explanation
Indices: 13513--13554 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
13503 TTAAAAATTT
13513 TTTATGAGTTTTG
1 TTTATGAGTTTTG
** *
13526 TTTAAAAATTTT-
1 TTTATGAGTTTTG
13538 TTTATGAGTTTTG
1 TTTATGAGTTTTG
13551 TTTA
1 TTTA
13555 AGAAGAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (13 bp):
TTTATGAGTTTTG
Found at i:13929 original size:41 final size:43
Alignment explanation
Indices: 13882--13967 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
13872 TTTTAATCTT
13882 CCATATATTTAGA-TTCTTTTC-ATGAGTTTATTCTTCTTTTC
1 CCATATATTTAGATTTCTTTTCTATGAGTTTATTCTTCTTTTC
*
13923 CCATATATTTAGATTTTTTTTCTATGAGTTTATTCTTCTTTTC
1 CCATATATTTAGATTTCTTTTCTATGAGTTTATTCTTCTTTTC
13966 CC
1 CC
13968 TTTTCATAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 13 0.31
42 7 0.17
43 22 0.52
ACGTcount: A:0.19, C:0.17, G:0.07, T:0.57
Consensus pattern (43 bp):
CCATATATTTAGATTTCTTTTCTATGAGTTTATTCTTCTTTTC
Found at i:13964 original size:21 final size:21
Alignment explanation
Indices: 13895--13965 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 21
13885 TATATTTAGA
13895 TTCTTTTC-ATGAGTTTATTC
1 TTCTTTTCTATGAGTTTATTC
13915 TTCTTTTCCCATAT-A-TTTAGATT-
1 TTCTTTT--C-TATGAGTTT--ATTC
13938 TT-TTTTCTATGAGTTTATTC
1 TTCTTTTCTATGAGTTTATTC
13958 TTCTTTTC
1 TTCTTTTC
13966 CCTTTTCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 19
0.68 0.00 0.32
Matches are distributed among these distances:
19 6 0.15
20 11 0.27
21 8 0.20
22 8 0.20
23 3 0.07
24 5 0.12
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.62
Consensus pattern (21 bp):
TTCTTTTCTATGAGTTTATTC
Found at i:13964 original size:22 final size:22
Alignment explanation
Indices: 13898--13964 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 22
13888 ATTTAGATTC
13898 TTTTC-ATGAGTTTATTCTTCT
1 TTTTCTATGAGTTTATTCTTCT
* *
13919 TTTCCCATAT-A-TTTAGAT-TT-T
1 TTT-TC-TATGAGTTTA-TTCTTCT
13940 TTTTCTATGAGTTTATTCTTCT
1 TTTTCTATGAGTTTATTCTTCT
13962 TTT
1 TTT
13965 CCCTTTTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 15
0.64 0.08 0.28
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 13 0.38
22 11 0.32
23 2 0.06
24 2 0.06
ACGTcount: A:0.16, C:0.13, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTCTATGAGTTTATTCTTCT
Found at i:17908 original size:4 final size:4
Alignment explanation
Indices: 17899--17924 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17889 ACCTTAAACC
17899 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
17925 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Done.