Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020171.1 Corchorus olitorius cultivar O-4 contig20204, 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: 16037
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2698 original size:29 final size:27
Alignment explanation
Indices: 2666--2741 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 27
2656 TCCAAATTGC
*
2666 AAGTTTAAGGTGCAAAACGTCCAAAATTA
1 AAGTTT-AGGGGCAAAACGT-CAAAATTA
2695 AAGTTTAGGGGCAAAACGTCAAAATCGTA
1 AAGTTTAGGGGCAAAACGTCAAAAT--TA
2724 CAAGTTTAGGGGGCAAAA
1 -AAGTTTA-GGGGCAAAA
2742 AGAGCTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
27 6 0.14
28 12 0.29
29 8 0.19
30 7 0.17
31 9 0.21
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (27 bp):
AAGTTTAGGGGCAAAACGTCAAAATTA
Found at i:3163 original size:6 final size:6
Alignment explanation
Indices: 3152--3181 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3142 AGCAACCCAT
3152 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG
3182 GTGGGGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.17, T:0.17
Consensus pattern (6 bp):
TCCCCG
Found at i:6236 original size:11 final size:11
Alignment explanation
Indices: 6206--6261 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
6196 TTATGCACCC
6206 AAAACATTTATT
1 AAAACATTTA-T
6218 AAAACATTTAT
1 AAAACATTTAT
*
6229 AAAGCATTTAT
1 AAAACATTTAT
*
6240 ATAAAGCAGTTAT
1 A-AAA-CATTTAT
6253 AAAACATTT
1 AAAACATTT
6262 CCTCAACGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 16 0.42
12 15 0.39
13 7 0.18
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:6244 original size:13 final size:13
Alignment explanation
Indices: 6210--6261 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
6200 GCACCCAAAA
*
6210 CATTTAT-TAAAA
1 CATTTATATAAAG
6222 CA-TT-TATAAAG
1 CATTTATATAAAG
6233 CATTTATATAAAG
1 CATTTATATAAAG
*
6246 CAGTTATA-AAA-
1 CATTTATATAAAG
6257 CATTT
1 CATTT
6262 CCTCAACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 12 0.35
12 7 0.21
13 14 0.41
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:6252 original size:24 final size:23
Alignment explanation
Indices: 6206--6261 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
6196 TTATGCACCC
*
6206 AAAACATTTATTAAAACATTTAT
1 AAAACATTTATTAAAACAGTTAT
* *
6229 AAAGCATTTATATAAAGCAGTTAT
1 AAAACATTTAT-TAAAACAGTTAT
6253 AAAACATTT
1 AAAACATTT
6262 CCTCAACGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (23 bp):
AAAACATTTATTAAAACAGTTAT
Found at i:7479 original size:3 final size:3
Alignment explanation
Indices: 7451--7495 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
7441 TTCATTCTTT
7451 TTA TT- TTA TT- TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7494 TT
1 TT
7496 TTAATTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 10 0.27
3 27 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (3 bp):
TTA
Found at i:7502 original size:6 final size:5
Alignment explanation
Indices: 7449--7498 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
7439 AATTCATTCT
7449 TTTTA TTTTA TTTTA TTTTA TTTTA --TTA TTATTA TTATTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA TTTTA TTTTA
7499 ATTTCTTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.07
5 28 0.67
6 11 0.26
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:7563 original size:30 final size:29
Alignment explanation
Indices: 7458--7563 Score: 71
Period size: 30 Copynumber: 3.6 Consensus size: 29
7448 TTTTTATTTT
*
7458 ATTTTATTTTATTTTATT-ATTATTATTATT-
1 ATTTTATTTTATTTT-TTCATT-TT-TCATTC
7488 ATTTTATTTTAATTTCTTTC--TTTTC-TTC
1 ATTTTATTTT-ATTT-TTTCATTTTTCATTC
**
7516 -TTCTTCATTTTCGTTTTTCATTTTTCATTC
1 ATT-TT-ATTTTATTTTTTCATTTTTCATTC
7546 ATTTTCATTTTATTTTTT
1 ATTTT-ATTTTATTTTTT
7564 TTAAAGTTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
27 8 0.13
28 5 0.08
29 12 0.20
30 27 0.44
31 8 0.13
32 1 0.02
ACGTcount: A:0.17, C:0.10, G:0.01, T:0.72
Consensus pattern (29 bp):
ATTTTATTTTATTTTTTCATTTTTCATTC
Found at i:10731 original size:21 final size:21
Alignment explanation
Indices: 10691--10732 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10681 ATTGGTGACG
* *
10691 TTGTTGGTTATTCATGCTATT
1 TTGTTGGTCATTCATACTATT
*
10712 TTGTTGGTCATTTATACTATT
1 TTGTTGGTCATTCATACTATT
10733 AGTATAGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (21 bp):
TTGTTGGTCATTCATACTATT
Found at i:11537 original size:21 final size:22
Alignment explanation
Indices: 11497--11537 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11487 TTAGGAGGTA
*
11497 GAAGTCAATATAGCATATATCC
1 GAAGTCAATACAGCATATATCC
*
11519 GAAGTC-ATACAGTATATAT
1 GAAGTCAATACAGCATATAT
11538 ATCAAGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (22 bp):
GAAGTCAATACAGCATATATCC
Done.