Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011451.1 Corchorus capsularis cultivar CVL-1 contig11472, 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: 29181
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:414 original size:16 final size:16
Alignment explanation
Indices: 393--423 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
383 AAATATACCA
*
393 AAAATACGAAAAGAAG
1 AAAATACAAAAAGAAG
409 AAAATACAAAAAGAA
1 AAAATACAAAAAGAA
424 AAAGCAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (16 bp):
AAAATACAAAAAGAAG
Found at i:516 original size:14 final size:13
Alignment explanation
Indices: 492--535 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
482 ATCGTAGAGT
492 AAAA-AGAAACGA
1 AAAATAGAAACGA
504 AAAATACGAAACGA
1 AAAATA-GAAACGA
518 AAAATAGAAAACGA
1 AAAATAG-AAACGA
532 AAAA
1 AAAA
536 ACAGAGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 23 0.79
ACGTcount: A:0.73, C:0.09, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAATAGAAACGA
Found at i:3122 original size:13 final size:13
Alignment explanation
Indices: 3104--3138 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
3094 ATAATTATTG
3104 TTTGCTTTATTAA
1 TTTGCTTTATTAA
3117 TTTGCTTTATTAA
1 TTTGCTTTATTAA
3130 TTTGCTTTA
1 TTTGCTTTA
3139 GATTTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:3520 original size:37 final size:37
Alignment explanation
Indices: 3450--3528 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 37
3440 TAGTTTTTGA
*
3450 TTTTCCGTTTTTTCTAAAAAAAAAAAAGGTTTTTCCGT
1 TTTTCCGATTTTTCTAAAAAAAAAAAA-GTTTTTCCGT
*
3488 TTTTCCGATTTTTCTAAAAAAAAAATTA-TTTTTCCGT
1 TTTTCCGATTTTTCTAAAAAAAAAA-AAGTTTTTCCGT
3525 TTTT
1 TTTT
3529 AAAATTAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 13 0.34
38 24 0.63
39 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (37 bp):
TTTTCCGATTTTTCTAAAAAAAAAAAAGTTTTTCCGT
Found at i:10232 original size:13 final size:13
Alignment explanation
Indices: 10214--10248 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
10204 ATAATTATTG
10214 TTTGCTTTATTAA
1 TTTGCTTTATTAA
10227 TTTGCTTTATTAA
1 TTTGCTTTATTAA
10240 TTTGCTTTA
1 TTTGCTTTA
10249 GATTTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:10256 original size:6 final size:6
Alignment explanation
Indices: 10245--10273 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
10235 ATTAATTTGC
10245 TTTAGA TTTAGA TTTAGA TTTAGA TTTAG
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAG
10274 GATTGCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TTTAGA
Found at i:10470 original size:33 final size:31
Alignment explanation
Indices: 10396--10506 Score: 89
Period size: 33 Copynumber: 3.4 Consensus size: 31
10386 CACATAAACC
* *
10396 CGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-GT
1 CGCGTGGCCGG-T-TGGCCGGACATGTCC-ATGT
** *
10429 CGTTTGGCCGGTTGAAGCCGGCCATGTCCATGT
1 CGCGTGGCCGGTTG--GCCGGACATGTCCATGT
*
10462 CGCGTGGCCGGTCATGGCTGGACATGTCCATGT
1 CGCGTGGCCGGT--TGGCCGGACATGTCCATGT
*
10495 CACGTGGCCGGT
1 CGCGTGGCCGGT
10507 CTTGTGGCCG
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.03
32 2 0.03
33 58 0.91
35 2 0.03
ACGTcount: A:0.10, C:0.28, G:0.40, T:0.23
Consensus pattern (31 bp):
CGCGTGGCCGGTTGGCCGGACATGTCCATGT
Found at i:15763 original size:17 final size:17
Alignment explanation
Indices: 15741--15777 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
15731 GTTATCCAGC
15741 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
15758 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
15775 ACC
1 ACC
15778 ATGAGGGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:23394 original size:20 final size:20
Alignment explanation
Indices: 23369--23408 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23359 AAACATGAAT
23369 AGAAGTATTATGAAAAACTA
1 AGAAGTATTATGAAAAACTA
*
23389 AGAAGTTTTATGAAAAACTA
1 AGAAGTATTATGAAAAACTA
23409 CTCACTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (20 bp):
AGAAGTATTATGAAAAACTA
Found at i:24213 original size:11 final size:11
Alignment explanation
Indices: 24197--24221 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24187 GTAAAAAGTT
24197 ATAATTTTTTA
1 ATAATTTTTTA
24208 ATAATTTTTTA
1 ATAATTTTTTA
24219 ATA
1 ATA
24222 TTCTTCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATAATTTTTTA
Found at i:24468 original size:20 final size:21
Alignment explanation
Indices: 24443--24485 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
24433 AAATTTGGTG
24443 TTGCTAAACACCGCCCCA-TT
1 TTGCTAAACACCGCCCCACTT
**
24463 TTGCTATTCACCGCCCCACTT
1 TTGCTAAACACCGCCCCACTT
24484 TT
1 TT
24486 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.19, C:0.40, G:0.09, T:0.33
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCACTT
Found at i:25923 original size:3 final size:3
Alignment explanation
Indices: 25915--25951 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
25905 CAACTTAATC
25915 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25952 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:26686 original size:1 final size:1
Alignment explanation
Indices: 26682--26707 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
26672 ATGCAAACGT
26682 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
26708 CTAGATCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26910 original size:11 final size:11
Alignment explanation
Indices: 26894--26918 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26884 TATAGTATAT
26894 ATAATATAATA
1 ATAATATAATA
26905 ATAATATAATA
1 ATAATATAATA
26916 ATA
1 ATA
26919 TAATTAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAATA
Found at i:26913 original size:16 final size:17
Alignment explanation
Indices: 26892--26936 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
26882 GATATAGTAT
26892 ATATAATATAATAA-TA
1 ATATAATATAATAATTA
26908 ATATAATA-ATATAATTA
1 ATATAATATA-ATAATTA
*
26925 AGA-AATATAATA
1 ATATAATATAATA
26937 GTATATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 19 0.76
17 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATAATATAATAATTA
Done.