Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020575.1 Corchorus olitorius cultivar O-4 contig20608, 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: 37186
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:264 original size:30 final size:27
Alignment explanation
Indices: 179--261 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
169 ATTAATTTAG
179 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
206 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
*
236 ACTTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
262 TTAGTGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:9553 original size:10 final size:10
Alignment explanation
Indices: 9538--9562 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9528 CTTTTTTGGG
9538 GCTTTATGGC
1 GCTTTATGGC
9548 GCTTTATGGC
1 GCTTTATGGC
9558 GCTTT
1 GCTTT
9563 TCCTGAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.20, G:0.28, T:0.44
Consensus pattern (10 bp):
GCTTTATGGC
Found at i:9864 original size:14 final size:14
Alignment explanation
Indices: 9832--9869 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
9822 ATGATTTGTA
*
9832 TATATGTAT-TATG
1 TATATATATGTATG
9845 TA-ATATATGTATG
1 TATATATATGTATG
9858 TATATATATGTA
1 TATATATATGTA
9870 CTTTTTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:17665 original size:29 final size:31
Alignment explanation
Indices: 17632--17696 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 31
17622 TCACATGTGC
17632 TTTTATAGTATC-A-ATAGCACATACCAATG
1 TTTTATAGTATCAAGATAGCACATACCAATG
17661 TTTTATAGTATCAACGGATAGCACATACCAATG
1 TTTTATAGTATCAA--GATAGCACATACCAATG
17694 TTT
1 TTT
17697 GTTGGGTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 12 0.38
30 1 0.03
33 19 0.59
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (31 bp):
TTTTATAGTATCAAGATAGCACATACCAATG
Found at i:25658 original size:15 final size:16
Alignment explanation
Indices: 25640--25671 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
25630 TTTAAGTTTC
25640 AGGGACTTAATT-AAA
1 AGGGACTTAATTGAAA
25655 AGGGACTTAATTGAAA
1 AGGGACTTAATTGAAA
25671 A
1 A
25672 TAAAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
AGGGACTTAATTGAAA
Found at i:26740 original size:18 final size:18
Alignment explanation
Indices: 26717--26759 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
26707 TATTTGAGAA
* *
26717 TTGCTGCCTATAATGTTG
1 TTGCTGACTAGAATGTTG
*
26735 TTGCTGATTAGAATGTTG
1 TTGCTGACTAGAATGTTG
26753 TTGCTGA
1 TTGCTGA
26760 TTTGAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.44
Consensus pattern (18 bp):
TTGCTGACTAGAATGTTG
Found at i:31857 original size:36 final size:36
Alignment explanation
Indices: 31810--31882 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
31800 TGTGAAGAGT
*
31810 GAGGCTTATGCTCATCTCTGTAGAAGTCCACCACGA
1 GAGGCTTATGCTCATCTCTGTAGAAGTCCAACACGA
31846 GAGGCTTATGCTCATCTCTGTAGAAGTCCAACACGA
1 GAGGCTTATGCTCATCTCTGTAGAAGTCCAACACGA
31882 G
1 G
31883 TATCGAAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (36 bp):
GAGGCTTATGCTCATCTCTGTAGAAGTCCAACACGA
Found at i:32115 original size:2 final size:2
Alignment explanation
Indices: 32108--32139 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32098 AATGCATCAT
32108 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
32140 AGTATTGGGT
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:32933 original size:64 final size:65
Alignment explanation
Indices: 32832--32955 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 65
32822 AGGTTAAATC
* * * *
32832 CTTTCAAGCCGACAGGATGAAAAGTTAAAGTCTTTCTAATAGATCCGTTTTTG-GGATCAAACTT
1 CTTTCAAGCCGACAGGATGAAAAGTTAAAATCCTTCTAACAAATCCGTTTTTGAGGATCAAACTT
* *
32896 CTTTCAAGCCGACAGGGT-AAGAAGTTAAAATCCTTCTAACAAATCTGTTTTTGAGGATCA
1 CTTTCAAGCCGACAGGATGAA-AAGTTAAAATCCTTCTAACAAATCCGTTTTTGAGGATCA
32956 GGGTGAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 2 0.04
64 44 0.85
65 6 0.12
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (65 bp):
CTTTCAAGCCGACAGGATGAAAAGTTAAAATCCTTCTAACAAATCCGTTTTTGAGGATCAAACTT
Found at i:35984 original size:14 final size:16
Alignment explanation
Indices: 35957--35989 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
35947 TGGCACCATT
35957 AAATATTTATATTATA
1 AAATATTTATATTATA
35973 AAAT-TTTA-ATTATA
1 AAATATTTATATTATA
35987 AAA
1 AAA
35990 CTAGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTTATATTATA
Done.