Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010973.1 Corchorus capsularis cultivar CVL-1 contig10994, 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: 31544
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:182 original size:21 final size:22
Alignment explanation
Indices: 123--170 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
113 GGACTTAGTC
123 TATTTATGTATAAAATATGCAA
1 TATTTATGTATAAAATATGCAA
145 TATTTATGTATAAAATATGCAA
1 TATTTATGTATAAAATATGCAA
167 TATT
1 TATT
171 ATTAAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (22 bp):
TATTTATGTATAAAATATGCAA
Found at i:1287 original size:41 final size:40
Alignment explanation
Indices: 1236--1565 Score: 315
Period size: 41 Copynumber: 7.8 Consensus size: 40
1226 ATATAGAAGT
* *
1236 TGCCTTTGTGTTATAATTGTGTTTAGGGACTTT-AGTATAGG
1 TGCCTCTGTGTTATAAATGTGTTT-GGGACTTTGA-TATAGG
* * *
1277 TGCCTTTGTGTGTTATAAATGTGCTTGAGGACTTTGAAATAGAG
1 TGCC--TCTGTGTTATAAATGTGTTTG-GGACTTTGATATAG-G
* *
1321 AT-ACTCATGTGTTATAAATGTGTTTGGGGACTTTGATATAGA
1 -TGCCTC-TGTGTTATAAATGTGTTT-GGGACTTTGATATAGG
* * * *
1363 TGTCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAA
1 TGCCTCTGTGTTATAAATGTGTTTG-GGACTTT-GATATAG-G
* *
1406 TCGCCCCTGTGTTATAAATGTGTTTGGGACTTTGATATAGA
1 T-GCCTCTGTGTTATAAATGTGTTTGGGACTTTGATATAGG
*
1447 TGCCTCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGA
1 TGCCTCTGTGTTATAAATGTGTTT-GGGACTTTGATATAGG
*
1488 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTG-TACGGAGAG
1 TGCCTCTGTGTTATAAATGTGTTTG-GGACTTTGATA--TAG-G
*
1531 TTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTG
1 -TGCCTCTGTGTTATAAATGTGTTT-GGGACTTTG
1566 GTTATTGGGT
Statistics
Matches: 249, Mismatches: 20, Indels: 37
0.81 0.07 0.12
Matches are distributed among these distances:
40 26 0.10
41 80 0.32
42 17 0.07
43 67 0.27
44 57 0.23
45 2 0.01
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (40 bp):
TGCCTCTGTGTTATAAATGTGTTTGGGACTTTGATATAGG
Found at i:1435 original size:84 final size:83
Alignment explanation
Indices: 1242--1565 Score: 370
Period size: 84 Copynumber: 3.8 Consensus size: 83
1232 AAGTTGCCTT
* * * *
1242 TGTGTTATAATTGTGTTTAGGGACTTT-AGTATAGGTGCCTTTGTGTGTTATAAATGTGCTTGAG
1 TGTGTTATAAATGTGTTTAGGGACTTTGA-TATAGATGCC--TCTGTGTTATAAATGTGTTTGAG
* * *
1306 GACTTTGAAATAGAGATACTCA
63 GACTTTGAAATAGA-ATGCCCC
* *
1328 TGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGTCTCTGTGTTATAAATGTGTTTGAGGAC
1 TGTGTTATAAATGTGTTTAGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC
*
1393 TTTAGAAAGAGAATCGCCCC
66 TTT-GAAATAGAAT-GCCCC
*
1413 TGTGTTATAAATGTGTTT-GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGGGGAC
1 TGTGTTATAAATGTGTTTAGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC
* *
1477 TTTGATATAG-ATGCCTC
66 TTTGAAATAGAATGCCCC
* *
1494 TGTGTTATAAATGTGTTT-GAGGACTTTG-TACGGAGAGTTGCCCCTGTGTTATAAATGTGTTTG
1 TGTGTTATAAATGTGTTTAG-GGACTTTGATA--TAGA--TGCCTCTGTGTTATAAATGTGTTTG
*
1557 GGGACTTTG
61 AGGACTTTG
1566 GTTATTGGGT
Statistics
Matches: 213, Mismatches: 17, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
81 25 0.12
82 10 0.05
83 8 0.04
84 76 0.36
85 60 0.28
86 33 0.15
87 1 0.00
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (83 bp):
TGTGTTATAAATGTGTTTAGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC
TTTGAAATAGAATGCCCC
Found at i:1495 original size:125 final size:126
Alignment explanation
Indices: 1285--1565 Score: 424
Period size: 125 Copynumber: 2.2 Consensus size: 126
1275 GGTGCCTTTG
*
1285 TGTGTTATAAATGTGCTTGAGGACTTTGAAATAGAGATACTCATGTGTTATAAATGTGTTTGGGG
1 TGTGTTATAAATGTGTTTG-GGACTTTGAAATAGAGA-ACTCATGTGTTATAAATGTGTTTGGGG
*
1350 ACTTTGATATAGATGTCTCTGTGTTATAAATGTGTTTGAGGACTTTAG-AAAGAGAATCGCCCC
64 ACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTT-GTAAAGAGAATCGCCCC
* *
1413 TGTGTTATAAATGTGTTTGGGACTTTGATATAGATG-CCTC-TGTGTTATAAATGTGTTTGGGGA
1 TGTGTTATAAATGTGTTTGGGACTTTGAAATAGA-GAACTCATGTGTTATAAATGTGTTTGGGGA
** * *
1476 CTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGTACGGAGAGTTGCCCC
65 CTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGTAAAGAGAATCGCCCC
1538 TGTGTTATAAATGTGTTTGGGGACTTTG
1 TGTGTTATAAATGTGTTT-GGGACTTTG
1566 GTTATTGGGT
Statistics
Matches: 142, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
124 1 0.01
125 96 0.68
126 12 0.08
127 14 0.10
128 19 0.13
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (126 bp):
TGTGTTATAAATGTGTTTGGGACTTTGAAATAGAGAACTCATGTGTTATAAATGTGTTTGGGGAC
TTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGTAAAGAGAATCGCCCC
Found at i:4636 original size:15 final size:14
Alignment explanation
Indices: 4616--4646 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4606 TACCCTTATC
4616 TTTTCTTTTTCGTTT
1 TTTTCTTTTTC-TTT
4631 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
4645 TT
1 TT
4647 ATTTTCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:7965 original size:21 final size:19
Alignment explanation
Indices: 7915--7965 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
7905 GGTAGCTAAC
*
7915 TTTTTTTAAAAAAGAAGTG
1 TTTTTTAAAAAAAGAAGTG
* *
7934 TTTTCATAAAAAGACGAAGTG
1 TTTT-TTAAAAA-AAGAAGTG
7955 TTTTTTAAAAA
1 TTTTTTAAAAA
7966 TATAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 11 0.42
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (19 bp):
TTTTTTAAAAAAAGAAGTG
Found at i:15004 original size:6 final size:6
Alignment explanation
Indices: 14993--15023 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
14983 CAAAGCAAAG
14993 TAAATC TAAATC TAAATC TAAATC TAAATC T
1 TAAATC TAAATC TAAATC TAAATC TAAATC T
15024 GAAGCAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:15981 original size:10 final size:10
Alignment explanation
Indices: 15966--15991 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15956 GAGGACTCTA
15966 GAATTTTCTG
1 GAATTTTCTG
15976 GAATTTTCTG
1 GAATTTTCTG
15986 GAATTT
1 GAATTT
15992 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:23069 original size:10 final size:10
Alignment explanation
Indices: 23054--23079 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23044 GAGGACTCTA
23054 GAATTTTCTG
1 GAATTTTCTG
23064 GAATTTTCTG
1 GAATTTTCTG
23074 GAATTT
1 GAATTT
23080 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:26712 original size:18 final size:18
Alignment explanation
Indices: 26689--26738 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
26679 AAGCTTCAGC
*
26689 TCTTGATGTCTCTCTTGG
1 TCTTGATGACTCTCTTGG
* *
26707 TCTTGATGAGTCTATTGG
1 TCTTGATGACTCTCTTGG
26725 TCTTGATGACTCTC
1 TCTTGATGACTCTC
26739 AAGCTGGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TCTTGATGACTCTCTTGG
Found at i:26748 original size:21 final size:21
Alignment explanation
Indices: 26722--26761 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
26712 ATGAGTCTAT
*
26722 TGGTCTTGATGACTCTCAAGC
1 TGGTCTTGATGACTATCAAGC
26743 TGGTCTTGATGACTATCAA
1 TGGTCTTGATGACTATCAA
26762 ATGTCTACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TGGTCTTGATGACTATCAAGC
Done.