Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016490.1 Corchorus olitorius cultivar O-4 contig16523, 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: 36943
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:2504 original size:78 final size:78
Alignment explanation
Indices: 2375--2533 Score: 300
Period size: 78 Copynumber: 2.0 Consensus size: 78
2365 AACAAGCTGT
*
2375 ATTTGGGATACAACAAAGCCGCTTAAGAATAACCAGAGAGAAGTAGAATTATTGGTGTGTAAAAA
1 ATTTGGGATACAACAAAGCCGCTTAAGAACAACCAGAGAGAAGTAGAATTATTGGTGTGTAAAAA
2440 TGGGAAAAAACAC
66 TGGGAAAAAACAC
*
2453 ATTTGGGATACAACAAAGCCGCTTAAGAACAACCAGAGAGAAGTATAATTATTGGTGTGTAAAAA
1 ATTTGGGATACAACAAAGCCGCTTAAGAACAACCAGAGAGAAGTAGAATTATTGGTGTGTAAAAA
2518 TGGGAAAAAACAC
66 TGGGAAAAAACAC
2531 ATT
1 ATT
2534 CTTATTTATA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (78 bp):
ATTTGGGATACAACAAAGCCGCTTAAGAACAACCAGAGAGAAGTAGAATTATTGGTGTGTAAAAA
TGGGAAAAAACAC
Found at i:6028 original size:17 final size:17
Alignment explanation
Indices: 6006--6064 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 17
5996 TGAAATATTT
6006 AAAACTTAATTAATTAA
1 AAAACTTAATTAATTAA
*
6023 AAAAC-TAGATTGAAATATTA
1 AAAACTTA-ATT--AAT-TAA
6043 AAAACTTAATTAATTTAA
1 AAAACTTAATTAA-TTAA
6061 AAAA
1 AAAA
6065 AATGGACATG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 8 0.24
19 4 0.12
20 10 0.29
21 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAACTTAATTAATTAA
Found at i:6030 original size:37 final size:38
Alignment explanation
Indices: 5989--6064 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
5979 TTATTTAGGG
*
5989 ACTAGATTGAAATATTTAAAACTTAATTAA-TTAAAAA
1 ACTAGATTGAAATATTAAAAACTTAATTAATTTAAAAA
6026 ACTAGATTGAAATATTAAAAACTTAATTAATTTAAAAA
1 ACTAGATTGAAATATTAAAAACTTAATTAATTTAAAAA
6064 A
1 A
6065 AATGGACATG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (38 bp):
ACTAGATTGAAATATTAAAAACTTAATTAATTTAAAAA
Found at i:6047 original size:20 final size:20
Alignment explanation
Indices: 5989--6048 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
5979 TTATTTAGGG
*
5989 ACTAGATTGAAATATTTAAA
1 ACTAGATTGAAATATTAAAA
*
6009 ACTTA-ATT--AAT-TAAAAA
1 AC-TAGATTGAAATATTAAAA
6026 ACTAGATTGAAATATTAAAA
1 ACTAGATTGAAATATTAAAA
6046 ACT
1 ACT
6049 TAATTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
16 2 0.06
17 9 0.28
18 3 0.09
19 3 0.09
20 13 0.41
21 2 0.06
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
ACTAGATTGAAATATTAAAA
Found at i:9195 original size:2 final size:2
Alignment explanation
Indices: 9188--9217 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9178 ACTAACGAAC
9188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9218 CTGAATCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10910 original size:31 final size:31
Alignment explanation
Indices: 10875--10933 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
10865 TTTCTTTCTG
10875 AATTTACAAAATCG-ACCTAATCTCCCCCCTA
1 AATTTACAAAATCGAACC-AATCTCCCCCCTA
*
10906 AATTTACAAAATGGAACCAATCTCCCCC
1 AATTTACAAAATCGAACCAATCTCCCCC
10934 AATCCAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.37, C:0.34, G:0.05, T:0.24
Consensus pattern (31 bp):
AATTTACAAAATCGAACCAATCTCCCCCCTA
Found at i:11554 original size:2 final size:2
Alignment explanation
Indices: 11549--11586 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11539 GAGAGAAAAC
11549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11587 TAATGTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12250 original size:24 final size:24
Alignment explanation
Indices: 12182--12247 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
12172 CTTATATATA
***
12182 TAATATATAATATATATACAATAAT
1 TAATATA-AATATATATTGGATAAT
* *
12207 TAATCTAATTATATATTGGATAAT
1 TAATATAAATATATATTGGATAAT
12231 TAATAATAAATATATAT
1 TAAT-ATAAATATATAT
12248 GGAAAAGACG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
24 17 0.52
25 16 0.48
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (24 bp):
TAATATAAATATATATTGGATAAT
Found at i:17460 original size:63 final size:63
Alignment explanation
Indices: 17251--17447 Score: 268
Period size: 63 Copynumber: 3.1 Consensus size: 63
17241 TGTAGGGGGT
* * * * * * * * *
17251 GGTGGCGTAAACGTGAACACAGGAAAAGGGAAGCCCAGCGGCACTTCGGTGAACGTTGGAAAA
1 GGTGGAGTAAATGTAAACACTGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAA
*
17314 GGTGGAGTAAATGTAAACACCGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAA
1 GGTGGAGTAAATGTAAACACTGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAA
* * * *
17377 GGTGGTGTAAATGTAAACACTGGGAAAGGAAAGCCCGGGGGAACTTCTGTTAATGTTGGAAAA
1 GGTGGAGTAAATGTAAACACTGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAA
17440 GGTGGAGT
1 GGTGGAGT
17448 TGGAGTGAAC
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 119 1.00
ACGTcount: A:0.33, C:0.15, G:0.34, T:0.18
Consensus pattern (63 bp):
GGTGGAGTAAATGTAAACACTGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAA
Found at i:25514 original size:2 final size:2
Alignment explanation
Indices: 25509--25539 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25499 CACAGACATG
*
25509 CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
25540 GCATATACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:32968 original size:57 final size:57
Alignment explanation
Indices: 32880--32995 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
32870 TGCTAAACCA
32880 AGTAATATAATAGATACATCCACAGACCATCAGGATCACAATATAGATATTTGCAAT
1 AGTAATATAATAGATACATCCACAGACCATCAGGATCACAATATAGATATTTGCAAT
32937 AGTAATATAATAGATACATCCACAGACCATCAGGATCACAATATAGATATTTGCAAT
1 AGTAATATAATAGATACATCCACAGACCATCAGGATCACAATATAGATATTTGCAAT
32994 AG
1 AG
32996 AGATACCAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (57 bp):
AGTAATATAATAGATACATCCACAGACCATCAGGATCACAATATAGATATTTGCAAT
Done.