Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015157.1 Corchorus capsularis cultivar CVL-1 contig15178, 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: 42872
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:1958 original size:22 final size:22
Alignment explanation
Indices: 1930--1971 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1920 ATTAGTAGCT
* *
1930 TCTTTTTATCGATCAAAAAGAC
1 TCTTTTTATCAATAAAAAAGAC
1952 TCTTTTTATCAATAAAAAAG
1 TCTTTTTATCAATAAAAAAG
1972 TTAGGGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTTTTTATCAATAAAAAAGAC
Found at i:6897 original size:15 final size:15
Alignment explanation
Indices: 6879--6908 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6869 CATGATGATA
6879 ATGACTATTATTATT
1 ATGACTATTATTATT
*
6894 ATGATTATTATTATT
1 ATGACTATTATTATT
6909 GCCGCCATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (15 bp):
ATGACTATTATTATT
Found at i:9750 original size:2 final size:2
Alignment explanation
Indices: 9739--9772 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9729 TTATTATTAC
9739 TA TA TA -A 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 TA TA TA TA T
9773 TGTCACATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11019 original size:20 final size:20
Alignment explanation
Indices: 10994--11032 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10984 TGGGGGACCA
10994 TTCATACTTTTAGGGCACAT
1 TTCATACTTTTAGGGCACAT
*
11014 TTCATACTTTTGGGGCACA
1 TTCATACTTTTAGGGCACA
11033 ATTGCACGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TTCATACTTTTAGGGCACAT
Found at i:13577 original size:2 final size:2
Alignment explanation
Indices: 13570--13598 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13560 ATAAATTGAT
13570 TA 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 TA T
13599 CTATTCATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21999 original size:7 final size:7
Alignment explanation
Indices: 21987--22014 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21977 ACCACGCCCG
21987 CACTAGT
1 CACTAGT
21994 CACTAGT
1 CACTAGT
22001 CACTAGT
1 CACTAGT
22008 CACTAGT
1 CACTAGT
22015 AGTCTACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
CACTAGT
Found at i:26849 original size:1 final size:1
Alignment explanation
Indices: 26843--26873 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
26833 CTAGTGAAAT
26843 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26874 CAAGATGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:31481 original size:6 final size:6
Alignment explanation
Indices: 31470--31496 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31460 TATGAGCCAA
31470 CTTTTC CTTTTC CTTTTC CTTTTC CTT
1 CTTTTC CTTTTC CTTTTC CTTTTC CTT
31497 CTTTTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
CTTTTC
Found at i:33711 original size:53 final size:53
Alignment explanation
Indices: 33625--33732 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
33615 TTAATCCTCA
*
33625 ATTTGACCTTTTAATAATTTCCATTATAGTTAAAAATAATATATAGTATATAT
1 ATTTGACCTTTTAATAATTTCCATTATAATTAAAAATAATATATAGTATATAT
* *
33678 ATTTGACCTTTTAGTAATTTCCATTGTAATTAAAAATAATATATAGTATATAT
1 ATTTGACCTTTTAATAATTTCCATTATAATTAAAAATAATATATAGTATATAT
33731 AT
1 AT
33733 ATTATAGGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (53 bp):
ATTTGACCTTTTAATAATTTCCATTATAATTAAAAATAATATATAGTATATAT
Found at i:35636 original size:56 final size:56
Alignment explanation
Indices: 35565--35684 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
35555 TAGAAAGGAA
*
35565 GAAAGTCCAAAGAAAATCATACAAATTAACCAGCTTACTTCTAGTTCAAATGATTG
1 GAAATTCCAAAGAAAATCATACAAATTAACCAGCTTACTTCTAGTTCAAATGATTG
*
35621 GAAATTCCAAAGAAAATCATACAAATTAACCAGCTTACTTCTAGTTCAAATTATTG
1 GAAATTCCAAAGAAAATCATACAAATTAACCAGCTTACTTCTAGTTCAAATGATTG
35677 GAAATTCC
1 GAAATTCC
35685 CCTAAGCTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.28
Consensus pattern (56 bp):
GAAATTCCAAAGAAAATCATACAAATTAACCAGCTTACTTCTAGTTCAAATGATTG
Found at i:39167 original size:2 final size:2
Alignment explanation
Indices: 39160--39191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39150 CTAGTGGCCA
39160 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
39192 TATCTAGGTG
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):
AT
Found at i:42531 original size:2 final size:2
Alignment explanation
Indices: 42524--42559 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42514 TTAACATTCT
42524 TA TA 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 TA TA
42560 ATGTAAAATA
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):
TA
Done.