Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014872.1 Corchorus olitorius cultivar O-4 contig14905, 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: 32036
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:402 original size:23 final size:24
Alignment explanation
Indices: 364--410 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
354 CAATTCAAGG
*
364 AAATTCAAATCTC-AAATAATCTCA
1 AAATTCAAATCACAAAATAA-CTCA
388 AAATTC-AATCACAAAATAACTCA
1 AAATTCAAATCACAAAATAACTCA
411 CTCAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATTCAAATCACAAAATAACTCA
Found at i:1145 original size:21 final size:20
Alignment explanation
Indices: 1093--1145 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1083 TATCTATAAT
* *
1093 TAAATATATATTTTATATATA
1 TAAA-ATATATATTACATATA
1114 TAAAATA-ATATTACATATA
1 TAAAATATATATTACATATA
1133 TAATAATATATAT
1 TAA-AATATATAT
1146 AATTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.46
20 7 0.25
21 8 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATATATATTACATATA
Found at i:1338 original size:69 final size:69
Alignment explanation
Indices: 1203--1338 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 69
1193 ACCGCATAGT
* * ** *
1203 CGGTTTAGGCGGTTAAATGGTCGGTTGACGGTTCCAAAAATTAGTCGTCGATTTGTAGTCGGTTT
1 CGGTTTAGGCGGTTAAATGGTCGGTTGACGATTCCAAAAATGAGTCGTCGATTTGTAACCGATTT
1268 TGTG
66 TGTG
*
1272 CGGTTTAGGCGGTTAAATGGTCGGTTGACGATTTCAAAAATGAGTCGTC-AGTTTGTAACCGATT
1 CGGTTTAGGCGGTTAAATGGTCGGTTGACGATTCCAAAAATGAGTCGTCGA-TTTGTAACCGATT
1336 TTG
65 TTG
1339 AGAACCACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.35
Consensus pattern (69 bp):
CGGTTTAGGCGGTTAAATGGTCGGTTGACGATTCCAAAAATGAGTCGTCGATTTGTAACCGATTT
TGTG
Found at i:1678 original size:15 final size:15
Alignment explanation
Indices: 1639--1672 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1629 TTGATAAAAT
*
1639 TGAAAA-TTAAGTGC
1 TGAAAAGTTAAGTAC
1653 TGAAAAGTTAAGTAC
1 TGAAAAGTTAAGTAC
1668 TGAAA
1 TGAAA
1673 TTTTAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (15 bp):
TGAAAAGTTAAGTAC
Found at i:2385 original size:69 final size:68
Alignment explanation
Indices: 2275--2410 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 68
2265 CAGATGATTT
* * *
2275 TGGATTTTTGTTTAGGCTAAAGAGTGGAAACCTAATTCCAATTTTT-TGAGATTAACGAGGAAGA
1 TGGATTTTTGTTTAGGCTAAAGAATGGAAACCTAATCCCAATTTTTCT-AGATTAACAAGGAAGA
2339 AGAC
65 AGAC
*
2343 TGGATTTTTCGTTTAGGCTAAAGAATGGAAACCTAATCCCAATTTTTCTAGATTAACAAGGAGGA
1 TGGATTTTT-GTTTAGGCTAAAGAATGGAAACCTAATCCCAATTTTTCTAGATTAACAAGGAAGA
2408 AGA
65 AGA
2411 AGACGATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
68 9 0.15
69 52 0.84
70 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (68 bp):
TGGATTTTTGTTTAGGCTAAAGAATGGAAACCTAATCCCAATTTTTCTAGATTAACAAGGAAGAA
GAC
Found at i:3006 original size:18 final size:18
Alignment explanation
Indices: 2979--3026 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2969 TAACGATTTA
2979 AATT-AATAATAATTAAT
1 AATTAAATAATAATTAAT
*
2996 AATTAAATAATTATTAAT
1 AATTAAATAATAATTAAT
*
3014 AATTAAAAAATAA
1 AATTAAATAATAA
3027 AAAAAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAATAATAATTAAT
Found at i:3027 original size:25 final size:25
Alignment explanation
Indices: 2979--3027 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2969 TAACGATTTA
* *
2979 AATTAATAATAATTAATAATTAAAT
1 AATTAATAATAATTAAAAAATAAAT
*
3004 AATTATTAATAATTAAAAAATAAA
1 AATTAATAATAATTAAAAAATAAA
3028 AAAAAATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATTAATAATAATTAAAAAATAAAT
Found at i:4497 original size:11 final size:11
Alignment explanation
Indices: 4481--4513 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
4471 CTGTGCTTCT
4481 GTGTTTTGGAA
1 GTGTTTTGGAA
4492 GTGTTTTGGAA
1 GTGTTTTGGAA
4503 GTGTTTTGGAA
1 GTGTTTTGGAA
4514 AAACATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (11 bp):
GTGTTTTGGAA
Found at i:13791 original size:41 final size:41
Alignment explanation
Indices: 13734--13817 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
13724 AGACCTAGCA
13734 ATTCGTGTATCCTTTTCGTGTTGTGTTTGGTCAGGTCATAG
1 ATTCGTGTATCCTTTTCGTGTTGTGTTTGGTCAGGTCATAG
13775 ATTCGTGTATCCTTTTCGTGTTGTGTTTGGTCAGGTCATAG
1 ATTCGTGTATCCTTTTCGTGTTGTGTTTGGTCAGGTCATAG
13816 AT
1 AT
13818 GTGTCATTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.13, C:0.14, G:0.26, T:0.46
Consensus pattern (41 bp):
ATTCGTGTATCCTTTTCGTGTTGTGTTTGGTCAGGTCATAG
Found at i:13896 original size:18 final size:19
Alignment explanation
Indices: 13858--13896 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13848 GTGTACTGTT
*
13858 GTTTCATCTCTCTTGTTTC
1 GTTTCATCTCTCATGTTTC
*
13877 GTTTCATGTCTCAT-TTTC
1 GTTTCATCTCTCATGTTTC
13895 GT
1 GT
13897 ATTATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.08, C:0.23, G:0.13, T:0.56
Consensus pattern (19 bp):
GTTTCATCTCTCATGTTTC
Found at i:22819 original size:17 final size:17
Alignment explanation
Indices: 22797--22830 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22787 TCCCTTTGAC
22797 CCGCCCTTCATTGGTAA
1 CCGCCCTTCATTGGTAA
22814 CCGCCCTTCATTGGTAA
1 CCGCCCTTCATTGGTAA
22831 GCTTGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (17 bp):
CCGCCCTTCATTGGTAA
Found at i:24901 original size:29 final size:30
Alignment explanation
Indices: 24836--24901 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
24826 TTATCAGATC
* *
24836 ATGAATCTTAATTTTTGACTCTAATAGGGTC
1 ATGAATCTTAATTTTT-ACTCCAATAGGGTA
*
24867 ATGAATCTTAATTTTT-C-CCACATAGTGTA
1 ATGAATCTTAATTTTTACTCCA-ATAGGGTA
24896 ATGAAT
1 ATGAAT
24902 TAAATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 13 0.42
31 16 0.52
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (30 bp):
ATGAATCTTAATTTTTACTCCAATAGGGTA
Found at i:27616 original size:2 final size:2
Alignment explanation
Indices: 27609--27639 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27599 AGAAGAGGGC
27609 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27640 AGCAAGCGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.