Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015695.1 Corchorus olitorius cultivar O-4 contig15728, 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: 58776
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2329 original size:30 final size:30
Alignment explanation
Indices: 2293--2353 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2283 CATTTGAAAA
2293 TGCTAAAAGATCAATTTGGTACCAAACGTT
1 TGCTAAAAGATCAATTTGGTACCAAACGTT
2323 TGCTAAAAGATCAATTTGGTACCAAACGTT
1 TGCTAAAAGATCAATTTGGTACCAAACGTT
2353 T
1 T
2354 ACCGAAATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (30 bp):
TGCTAAAAGATCAATTTGGTACCAAACGTT
Found at i:3003 original size:10 final size:10
Alignment explanation
Indices: 2988--3014 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2978 CCACAATTTA
2988 ATTTTCTTTT
1 ATTTTCTTTT
2998 ATTTTCTTTT
1 ATTTTCTTTT
3008 ATTTTCT
1 ATTTTCT
3015 CATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (10 bp):
ATTTTCTTTT
Found at i:3477 original size:6 final size:5
Alignment explanation
Indices: 3445--3483 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3435 TCAAATCATT
* * *
3445 AAAGG AAAGG AAAGA AAATG AAAGG AAAGG GAAGG AAAG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAG
3484 TTTTTTAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (5 bp):
AAAGG
Found at i:5844 original size:13 final size:13
Alignment explanation
Indices: 5826--5853 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5816 ATTTGTGTCT
5826 AGAAATAAGTTTG
1 AGAAATAAGTTTG
5839 AGAAATAAGTTTG
1 AGAAATAAGTTTG
5852 AG
1 AG
5854 TTGCACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (13 bp):
AGAAATAAGTTTG
Found at i:14541 original size:31 final size:31
Alignment explanation
Indices: 14470--14541 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
14460 GTCTATCATC
*
14470 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* *
14501 TCATT-ATTTGTTTAATTTAATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTAATTT
14531 GTTTTAATTTG
1 -TTTTAATTTG
14542 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:14847 original size:37 final size:38
Alignment explanation
Indices: 14781--14852 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 38
14771 TATTCAATCT
* *
14781 TTATATATATATATTGATAATCATGTTATATTATATTA
1 TTATATATATATATTGATAATAATGTTATAATATATTA
14819 TTATAT-TATATATT-ATCAATAAAT-TTATAATATA
1 TTATATATATATATTGAT-AAT-AATGTTATAATATA
14853 AAAGATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
36 2 0.07
37 20 0.67
38 8 0.27
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
TTATATATATATATTGATAATAATGTTATAATATATTA
Found at i:15027 original size:15 final size:16
Alignment explanation
Indices: 14994--15031 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
14984 CCGAAAATAT
*
14994 CCAAACCCGACATAGC
1 CCAAACCCGACAAAGC
15010 CCAAACCCGA-AAAGC
1 CCAAACCCGACAAAGC
15025 CCAAACC
1 CCAAACC
15032 TAAAGTACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.45, G:0.11, T:0.03
Consensus pattern (16 bp):
CCAAACCCGACAAAGC
Found at i:21329 original size:42 final size:43
Alignment explanation
Indices: 21278--21365 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 43
21268 TGCATTACCT
* *
21278 AAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
*
21320 AAATTCTACTCCTCCATCTCTAGATAATTCATTAAAATAAAACTA
1 AAATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTA
21365 A
1 A
21366 TATTAATTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 8 0.20
45 32 0.80
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.32
Consensus pattern (43 bp):
AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:28724 original size:17 final size:16
Alignment explanation
Indices: 28693--28733 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
28683 TCACGCCAAA
*
28693 AAATAATTAATAAAAT
1 AAATAAATAATAAAAT
28709 AAATAAATAGATAAAAT
1 AAATAAATA-ATAAAAT
28726 AAAGTAAA
1 AAA-TAAA
28734 CTACCAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 10 0.45
18 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
AAATAAATAATAAAAT
Found at i:53432 original size:101 final size:105
Alignment explanation
Indices: 53244--53445 Score: 299
Period size: 108 Copynumber: 1.9 Consensus size: 105
53234 TGTGTTTTGG
53244 TTTTTTTTTTTAATTTTTTTTTTACTTTGTACAAACATCATCTAGTCGTATTCAGTCCCATCCAT
1 TTTTTTTTTTTAATTTTTTTTTTACTTTGTACAAACATCATCTAGTCGTATTCAGTCCCATCCAT
53309 CATCCATCATCCATCCCCCAAACACACACTTTATATTGGATT
66 CATCCA-CATCCAT-CCCCAAACACACACTTTATATTGGATT
** *
53351 TTTTTTTTTTTTTTTTTGTCTTTTTAC-TTGTACAAACATCATCTTGTCGTATTCAGTCCCATCC
1 TTTTTTTTTTTAATTTT-T-TTTTTACTTTGTACAAACATCATCTAGTCGTATTCAGTCCCATCC
53415 ATCAT-C-CAT-C-T-CCCAAACACACACTTTATAT
64 ATCATCCACATCCATCCCCAAACACACACTTTATAT
53446 ATAAAGAAAT
Statistics
Matches: 90, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
101 20 0.22
103 1 0.01
104 1 0.01
105 3 0.03
107 16 0.18
108 42 0.47
109 7 0.08
ACGTcount: A:0.24, C:0.25, G:0.05, T:0.46
Consensus pattern (105 bp):
TTTTTTTTTTTAATTTTTTTTTTACTTTGTACAAACATCATCTAGTCGTATTCAGTCCCATCCAT
CATCCACATCCATCCCCAAACACACACTTTATATTGGATT
Done.