Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008796.1 Corchorus capsularis cultivar CVL-1 contig08817, 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: 38412
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:804 original size:1 final size:1
Alignment explanation
Indices: 798--826 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
788 TTTAGGCACC
798 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
827 CCGAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1999 original size:23 final size:23
Alignment explanation
Indices: 1973--2022 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1963 TTTTTGCATC
1973 ATCTGATATATTGTCAGTTCATA
1 ATCTGATATATTGTCAGTTCATA
*
1996 ATCTGATATATTGTTAGTTCATA
1 ATCTGATATATTGTCAGTTCATA
2019 ATCT
1 ATCT
2023 TCATGTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (23 bp):
ATCTGATATATTGTCAGTTCATA
Found at i:6722 original size:24 final size:24
Alignment explanation
Indices: 6694--6746 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
6684 TGAAGATGAA
*
6694 GATGAGAATATGAGTGAGGGAACC
1 GATGAGAATATGAATGAGGGAACC
*
6718 GATGAGGATATGAATGAGGGAACC
1 GATGAGAATATGAATGAGGGAACC
6742 GATGA
1 GATGA
6747 AGTTGAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.17
Consensus pattern (24 bp):
GATGAGAATATGAATGAGGGAACC
Found at i:9434 original size:10 final size:8
Alignment explanation
Indices: 9404--9435 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
9394 ACAATGTTAA
9404 TCTTTTCC
1 TCTTTTCC
9412 TCTTTTCC
1 TCTTTTCC
9420 TCTTTTCC
1 TCTTTTCC
9428 TCTCTTTC
1 TCT-TTTC
9436 TATTTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (8 bp):
TCTTTTCC
Found at i:10288 original size:43 final size:43
Alignment explanation
Indices: 10204--10288 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
10194 CATTACAAAA
* * *
10204 TGGGGACCACCTTTTCAGATGAATCAAAATCTGTGTCTGGGAT
1 TGGGGACCAACTTTTCAGATGAATCAAAATATGGGTCTGGGAT
* * *
10247 TGGGGACCAATTTTTCTGATGAATCAAAATATGGGTTTGGGA
1 TGGGGACCAACTTTTCAGATGAATCAAAATATGGGTCTGGGA
10289 CAAAAATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (43 bp):
TGGGGACCAACTTTTCAGATGAATCAAAATATGGGTCTGGGAT
Found at i:13001 original size:29 final size:29
Alignment explanation
Indices: 12951--13022 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
12941 TTAGGTTGAT
12951 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
1 GGGGCAAAACGTCCCAAAATTGAAGTTC-G
* *
12981 GGGGCAAAATGT-CCAAGATTGAAGTTCG
1 GGGGCAAAACGTCCCAAAATTGAAGTTCG
13009 GGGGACAAAACGTC
1 GGGG-CAAAACGTC
13023 TAGACGCTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.14
29 21 0.57
30 11 0.30
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.17
Consensus pattern (29 bp):
GGGGCAAAACGTCCCAAAATTGAAGTTCG
Found at i:16354 original size:5 final size:5
Alignment explanation
Indices: 16344--16379 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
16334 CCATCTGAAA
*
16344 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT CTGTT T
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT T
16380 CTTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.78
Consensus pattern (5 bp):
TTGTT
Found at i:17094 original size:6 final size:6
Alignment explanation
Indices: 17087--17162 Score: 125
Period size: 6 Copynumber: 12.7 Consensus size: 6
17077 ATTAACGGCC
* * *
17087 GAGGCC GAGGCC GAGGCC GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT
1 GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT
17135 GAGGCT GAGGCT GAGGCT GAGGCT GAGG
1 GAGGCT GAGGCT GAGGCT GAGGCT GAGG
17163 TGGTGTAAGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.17, C:0.20, G:0.51, T:0.12
Consensus pattern (6 bp):
GAGGCT
Found at i:17755 original size:20 final size:21
Alignment explanation
Indices: 17730--17775 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
17720 TCAAAATAAA
*
17730 ATAAAAACTACCCATTTTA-G
1 ATAAAAACTACCCATTATAGG
*
17750 ATAAAAACTACTCATTATAGG
1 ATAAAAACTACCCATTATAGG
17771 ATAAA
1 ATAAA
17776 TATAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (21 bp):
ATAAAAACTACCCATTATAGG
Found at i:20342 original size:5 final size:5
Alignment explanation
Indices: 20332--20364 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20322 CCCATCTTCA
*
20332 TGCCC TGCCC TGCCC TGCCC TGCCC TGCTC TGC
1 TGCCC TGCCC TGCCC TGCCC TGCCC TGCCC TGC
20365 GTGTAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.55, G:0.21, T:0.24
Consensus pattern (5 bp):
TGCCC
Found at i:34427 original size:19 final size:18
Alignment explanation
Indices: 34403--34446 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
34393 CACAAAATAC
34403 AAAAAAAGAAAAAAATTTA
1 AAAAAAAGAAAAAAA-TTA
* *
34422 AAAAAAAGAAGAAGATTA
1 AAAAAAAGAAAAAAATTA
34440 AAAAAAA
1 AAAAAAA
34447 CGAATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAAAAAGAAAAAAATTA
Found at i:36551 original size:13 final size:13
Alignment explanation
Indices: 36528--36558 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
36518 TTAATACAGG
36528 TATCG-ACGGATA
1 TATCGAACGGATA
36540 TATCGAACGGATA
1 TATCGAACGGATA
36553 TATCGA
1 TATCGA
36559 GGTATCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:37440 original size:10 final size:10
Alignment explanation
Indices: 37425--37473 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
37415 TTTAATTTAA
*
37425 TATGGATGTT
1 TATGGATATT
37435 TATGGATATT
1 TATGGATATT
37445 TATGGATATT
1 TATGGATATT
*
37455 TACGGATATT
1 TATGGATATT
*
37465 TACGGATAT
1 TATGGATAT
37474 ATCGAGAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.45
Consensus pattern (10 bp):
TATGGATATT
Done.