Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013126.1 Corchorus olitorius cultivar O-4 contig13159, 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: 24351
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:252 original size:11 final size:11
Alignment explanation
Indices: 236--261 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
226 AGATAATTTC
236 TTTTCTTCTAG
1 TTTTCTTCTAG
247 TTTTCTTCTAG
1 TTTTCTTCTAG
258 TTTT
1 TTTT
262 TTAGGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:1045 original size:15 final size:15
Alignment explanation
Indices: 1016--1056 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1006 TATTTTGCTT
1016 TGTTTTCTAGTTTAAA
1 TGTTTTCT-GTTTAAA
*
1032 TGTTTTCTGTTTAAT
1 TGTTTTCTGTTTAAA
*
1047 TGCTTTCTGT
1 TGTTTTCTGT
1057 CAACCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (15 bp):
TGTTTTCTGTTTAAA
Found at i:4725 original size:21 final size:21
Alignment explanation
Indices: 4699--4753 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
4689 CGCCCATTCA
4699 CCGTGCCACCACCGG-TCAAGC
1 CCGTGCCACCACCGGCT-AAGC
* *
4720 CCGTGCCACCACTGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
4741 CCGTGCCATCACC
1 CCGTGCCACCACC
4754 ATTCCAAGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:8635 original size:15 final size:15
Alignment explanation
Indices: 8605--8646 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
8595 TTACTTTGCT
8605 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
8621 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
8636 TTGCTTTCTGT
1 TTGTTTTCTGT
8647 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:10612 original size:26 final size:28
Alignment explanation
Indices: 10561--10614 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
10551 GGCCATTTTC
* *
10561 ATGTGTTGGGCATCTTTTTGTGTATGTG
1 ATGTATTGGGCATCTTTTTGTATATGTG
10589 ATGTATTGGGC-TCTTTTT-TATATGTG
1 ATGTATTGGGCATCTTTTTGTATATGTG
10615 TGTGATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 7 0.29
28 10 0.42
ACGTcount: A:0.13, C:0.07, G:0.28, T:0.52
Consensus pattern (28 bp):
ATGTATTGGGCATCTTTTTGTATATGTG
Found at i:14674 original size:24 final size:24
Alignment explanation
Indices: 14599--14675 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
14589 TTTGCGGTAT
14599 AATTGTGGTTGGCTTCTACCGCA-
1 AATTGTGGTTGGCTTCTACCGCAG
* * * *
14622 AACTATGGTGCTTGACTTCTACGGTAG
1 AA-T-T-GTGGTTGGCTTCTACCGCAG
*
14649 AATTGTGGTTGGCTTCTGCCGCAG
1 AATTGTGGTTGGCTTCTACCGCAG
14673 AAT
1 AAT
14676 GGTGCTGCTT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 2 0.05
26 16 0.39
27 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (24 bp):
AATTGTGGTTGGCTTCTACCGCAG
Found at i:15704 original size:42 final size:41
Alignment explanation
Indices: 15614--15708 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 41
15604 ATGTGGCTAT
* * *
15614 AGAGAAAGACACTCCTATAGTTGACACTGATGCTGCGGTTA
1 AGAGAAGGACACTCCCACAGTTGACACTGATGCTGCGGTTA
* * * * *
15655 GGCAGAAGGACATTCCCACAGTTGAGACTGTTGTTGCGGTTAA
1 AG-AGAAGGACACTCCCACAGTTGACACTGATGCTGCGGTT-A
15698 AGAGAAGGACA
1 AGAGAAGGACA
15709 ACGACATTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
41 1 0.02
42 40 0.93
43 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (41 bp):
AGAGAAGGACACTCCCACAGTTGACACTGATGCTGCGGTTA
Found at i:15985 original size:27 final size:27
Alignment explanation
Indices: 15891--16191 Score: 186
Period size: 27 Copynumber: 11.0 Consensus size: 27
15881 AGAGAAAGAT
*
15891 GCTCCCGCAGTTGGGACTCATGTGGAA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
* * *
15918 -CTCCCGCAATTGGGATCGAACTCACGCTATGCA
1 GCTCCCGCAGTT-GG---G-ACTCATG-T-TGAA
* *
15951 GCTTCCGCAGTTGGGACTCACGTTGAA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
* *
15978 GCTCCCGCAGTTGGGACTCACGTTATAAA
1 GCTCCCGCAGTTGGGACTCATG-T-TGAA
* * *
16007 ACT-CC-CA--TAGGACTCATGATGAA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
** * * *
16030 GCTCCCATAGTTGAGATTCATGCTGAA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
* * *
16057 GCTCCCGCAGTCGGGACTCATGCTGTA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
* * *
16084 GCTCCCGTAGTCGGGACTCATG-TCAA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
* *
16110 GGC-CTCCGCAGTTGGGACTCATGCTGCA
1 -GCTC-CCGCAGTTGGGACTCATGTTGAA
* ***
16138 GCTCCCGCAGTCGGGACTCATGCCAAA
1 GCTCCCGCAGTTGGGACTCATGTTGAA
16165 GC-CTCCGCAGTTGGGACTCATGTTGAA
1 GCTC-CCGCAGTTGGGACTCATGTTGAA
16192 CGTATGATGT
Statistics
Matches: 214, Mismatches: 41, Indels: 38
0.73 0.14 0.13
Matches are distributed among these distances:
23 5 0.02
24 2 0.01
25 10 0.05
26 14 0.07
27 142 0.66
28 7 0.03
29 12 0.06
30 2 0.01
31 6 0.03
32 1 0.00
33 4 0.02
34 9 0.04
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (27 bp):
GCTCCCGCAGTTGGGACTCATGTTGAA
Found at i:16181 original size:81 final size:81
Alignment explanation
Indices: 16038--16187 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 81
16028 AAGCTCCCAT
* *** *
16038 AGTTGAGATTCATGCTGAAGCTCCCGCAGTCGGGACTCATGCTGTAGCTCCCGTAGTCGGGACTC
1 AGTTGAGACTCATGCTGAAGCTCCCGCAGTCGGGACTCATGCCAAAGCTCCCGCAGTCGGGACTC
16103 ATGTCAAGGCCTCCGC
66 ATGTCAAGGCCTCCGC
* * *
16119 AGTTGGGACTCATGCTGCAGCTCCCGCAGTCGGGACTCATGCCAAAGC-CTCCGCAGTTGGGACT
1 AGTTGAGACTCATGCTGAAGCTCCCGCAGTCGGGACTCATGCCAAAGCTC-CCGCAGTCGGGACT
16183 CATGT
65 CATGT
16188 TGAACGTATG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.02
81 59 0.98
ACGTcount: A:0.19, C:0.30, G:0.29, T:0.23
Consensus pattern (81 bp):
AGTTGAGACTCATGCTGAAGCTCCCGCAGTCGGGACTCATGCCAAAGCTCCCGCAGTCGGGACTC
ATGTCAAGGCCTCCGC
Found at i:16254 original size:27 final size:26
Alignment explanation
Indices: 16202--16282 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
16192 CGTATGATGT
* *
16202 TGAAGCTCCGCAGTTGGAACTTATGC
1 TGAAGCTCCGCAGTAGGAACTCATGC
16228 TGAAGCTCCCGCAGTAAGG-ACTCATGC
1 TGAAGCT-CCGCAGT-AGGAACTCATGC
** * * *
16255 CAAAGCCTCTGCAGTTGGGACTCATGC
1 TGAAG-CTCCGCAGTAGGAACTCATGC
16282 T
1 T
16283 ATAAAACTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 9 0.20
27 31 0.70
28 4 0.09
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.23
Consensus pattern (26 bp):
TGAAGCTCCGCAGTAGGAACTCATGC
Done.