Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008431.1 Corchorus capsularis cultivar CVL-1 contig08452, 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: 21731
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1943 original size:8 final size:8
Alignment explanation
Indices: 1932--2023 Score: 73
Period size: 8 Copynumber: 11.5 Consensus size: 8
1922 ACTAAAATTT
1932 AAAAAAAG
1 AAAAAAAG
1940 AAAACAAA-
1 AAAA-AAAG
1948 ACAAAAAA-
1 A-AAAAAAG
1956 AAACAAAAG
1 AAA-AAAAG
*
1965 AAAGAAAG
1 AAAAAAAG
*
1973 AAAGAAAG
1 AAAAAAAG
*
1981 AAAGAAAG
1 AAAAAAAG
*
1989 AAAGAAAG
1 AAAAAAAG
*
1997 AAGAAAAG
1 AAAAAAAG
*
2005 AAAAGAA-
1 AAAAAAAG
*
2012 AAGAAAAG
1 AAAAAAAG
2020 AAAA
1 AAAA
2024 GGTTTGCAGT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
7 7 0.10
8 55 0.77
9 9 0.13
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1968 original size:4 final size:4
Alignment explanation
Indices: 1961--2022 Score: 81
Period size: 4 Copynumber: 14.8 Consensus size: 4
1951 AAAAAAAACA
1961 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAAAG AAAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG -AAAG
2010 AAAAG AAAAG AAA
1 -AAAG -AAAG AAA
2023 AGGTTTGCAG
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.05
4 35 0.62
5 18 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2007 original size:5 final size:5
Alignment explanation
Indices: 1935--2024 Score: 77
Period size: 5 Copynumber: 19.0 Consensus size: 5
1925 AAAATTTAAA
* * * *
1935 AAAAG AAAAC AAAAC AAAAA AAAAC AAAAG -AAAG -AAAG -AAAG -AAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1981 -AAAG -AAAG -AAAG AAAGAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG -AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG
2025 GTTTGCAGTC
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
4 28 0.36
5 44 0.56
6 3 0.04
7 3 0.04
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3946 original size:17 final size:17
Alignment explanation
Indices: 3926--3976 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
3916 TCATGATTAA
3926 TATGTTTGCTCAATAAT
1 TATGTTTGCTCAATAAT
*
3943 TATGTGTG--CAAT-A-
1 TATGTTTGCTCAATAAT
*
3956 CATGTTTGCTCAATAAT
1 TATGTTTGCTCAATAAT
3973 TATG
1 TATG
3977 GTATGTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 6 0.23
14 1 0.04
15 8 0.31
16 1 0.04
17 10 0.38
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (17 bp):
TATGTTTGCTCAATAAT
Found at i:6468 original size:9 final size:9
Alignment explanation
Indices: 6457--6495 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
6447 GCAAAAAATA
6457 AAAAATAA-
1 AAAAATAAT
6465 AAAAATAAT
1 AAAAATAAT
*
6474 AATAATAAT
1 AAAAATAAT
*
6483 AATAATAAT
1 AAAAATAAT
6492 AAAA
1 AAAA
6496 CCCATTGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATAAT
Found at i:6474 original size:3 final size:3
Alignment explanation
Indices: 6468--6493 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6458 AAAATAAAAA
6468 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6494 AACCCATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11659 original size:21 final size:21
Alignment explanation
Indices: 11616--11659 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11606 TAAAAAGGGG
*
11616 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCTACTT
11637 TTGCTAAATACCGTCCC-ACTT
1 TTGCTAAATACCG-CCCTACTT
11658 TT
1 TT
11660 TACACTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCTACTT
Found at i:14601 original size:19 final size:19
Alignment explanation
Indices: 14577--14615 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
14567 GTTAAAAGAG
* *
14577 TGAGTAGGATGAGAGAGAA
1 TGAGTAGGAGGAAAGAGAA
14596 TGAGTAGGAGGAAAGAGAA
1 TGAGTAGGAGGAAAGAGAA
14615 T
1 T
14616 AGGGGCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (19 bp):
TGAGTAGGAGGAAAGAGAA
Found at i:16527 original size:109 final size:109
Alignment explanation
Indices: 16370--16703 Score: 564
Period size: 109 Copynumber: 3.1 Consensus size: 109
16360 TCTACATTCA
* *
16370 AGTTTACTG-TTTCTCGATTAATAGGTAATG-AATTTTCTGTTCTGGTTCATGTGATTTATGATG
1 AGTTTACTGTTTTCT-GATTAATAGGTACTGAAATTTT-TGTTGTGGTTCATGTGATTTATGATG
*
16433 AAGGCTAATCTGATATCATGCATCAATGATGCATCTAAGAGCAAAG
64 AAGGCTAATCTGTTATCATGCATCAATGATGCATCTAAGAGCAAAG
*
16479 AGTTTACTGTTTTCTGATTAATAGGTACTGAAATTTTTGTTGTAGTTCATGTGATTTATGATGAA
1 AGTTTACTGTTTTCTGATTAATAGGTACTGAAATTTTTGTTGTGGTTCATGTGATTTATGATGAA
16544 GGCTAATCTGTTATCATGCATCAATGATGCATCTAAGAGCAAAG
66 GGCTAATCTGTTATCATGCATCAATGATGCATCTAAGAGCAAAG
*
16588 AGTTTACTGTTTTCTGATTAATAGGTACTGAAATTTTTGTTGTGGTTCATGTGATTTATGATGTA
1 AGTTTACTGTTTTCTGATTAATAGGTACTGAAATTTTTGTTGTGGTTCATGTGATTTATGATGAA
* *
16653 GGCTAATCTGTTATCATGCATAAATGATGCATTTAAGAGCAAAG
66 GGCTAATCTGTTATCATGCATCAATGATGCATCTAAGAGCAAAG
16697 AGCTTTA
1 AG-TTTA
16704 ACTTCTATAA
Statistics
Matches: 214, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
109 199 0.93
110 15 0.07
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (109 bp):
AGTTTACTGTTTTCTGATTAATAGGTACTGAAATTTTTGTTGTGGTTCATGTGATTTATGATGAA
GGCTAATCTGTTATCATGCATCAATGATGCATCTAAGAGCAAAG
Found at i:16914 original size:39 final size:36
Alignment explanation
Indices: 16853--16928 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 36
16843 AAACCCACGG
*
16853 TGGTTCTGGGCGGTGGGTGAAGAGTTCCGATATTGC
1 TGGTTCTGGGCGGTGGATGAAGAGTTCCGATATTGC
* *
16889 TGGTTCTGGGCAGTGGTGGATGAAGATTTCTGATATTGC
1 TGGTTCTGGGC---GGTGGATGAAGAGTTCCGATATTGC
16928 T
1 T
16929 AAAAGGAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.32
39 23 0.68
ACGTcount: A:0.16, C:0.12, G:0.38, T:0.34
Consensus pattern (36 bp):
TGGTTCTGGGCGGTGGATGAAGAGTTCCGATATTGC
Found at i:17800 original size:22 final size:21
Alignment explanation
Indices: 17772--17828 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
17762 TGCGAAGTTC
*
17772 GAAGATTATTTGAAGATAATTT
1 GAAGATTATTTGAAGACAA-TT
17794 GAAG---ATTTGAAGACAATT
1 GAAGATTATTTGAAGACAATT
*
17812 GAAGAATTATTTCAAGA
1 GAAG-ATTATTTGAAGA
17829 AGCAAGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
22 12 0.41
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (21 bp):
GAAGATTATTTGAAGACAATT
Found at i:17803 original size:19 final size:18
Alignment explanation
Indices: 17779--17816 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17769 TTCGAAGATT
*
17779 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
17798 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
17816 A
1 A
17817 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:21189 original size:35 final size:34
Alignment explanation
Indices: 21056--21726 Score: 792
Period size: 35 Copynumber: 19.7 Consensus size: 34
21046 AGTAATAAGA
21056 AACTTAATTCAGGGTAATTAAGTAAGTCAG----C
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
*
21087 AACTTAATTCAGGGTAATT-A--AATAAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATCAGTAATC
*
21118 AACTTAATTCAGAGTAATTAAGT-A--AGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATCAGTAATC
21149 AACTTAATTCAGGGTAATTAAGTAATTCAGTAAT-
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
* *
21183 AGACTTAATTCAGGGTAATTAAGCGAGTCAGTAATAAGC
1 A-ACTTAATTCAGGGTAATTAAG-TAATCAGTAAT---C
21222 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
* *
21257 AACTTAATTCAGGGTAATTAAGTGAGTCAATAATC
1 AACTTAATTCAGGGTAATTAAGT-AATCAGTAATC
21292 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
*
21327 AACTTAATTCACGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
* *
21362 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAAGC
1 AACTTAATTCAGGGTAATTAAGT-AATCAGTAATC
*
21397 AACATAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
* **
21432 AACTTAATTCAGGGTAATTAAGCGAGCCAGTAATC
1 AACTTAATTCAGGGTAATTAAG-TAATCAGTAATC
21467 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAA-TCAGTAATC
*
21502 AACTTAATT-AGGGTAATTAAGTGGATCAGTAATC
1 AACTTAATTCAGGGTAATTAAGT-AATCAGTAATC
*
21536 AACTTAATTCAGGGTAATTAAGTGAGTCAGTGAAT-
1 AACTTAATTCAGGGTAATTAAGT-AATCAGT-AATC
21571 AACTTAATTCAGGGTAATTAAG---TCAGTAAAT-
1 AACTTAATTCAGGGTAATTAAGTAATCAGT-AATC
* *
21602 AGCTTAATTCAGGGTAATTAAGTGAGTCAGTTAAT-
1 AACTTAATTCAGGGTAATTAAGT-AATCAG-TAATC
*
21637 GACTTAATTCAGGGTAATTAAG---TCAGTAAGT-
1 AACTTAATTCAGGGTAATTAAGTAATCAGTAA-TC
* *
21668 AGCTTAATTAAGGGTAATTAAGTGAATCAGTAATC
1 AACTTAATTCAGGGTAATTAAGT-AATCAGTAATC
21703 AACTTTAATTCAGGGTAATTAAGT
1 AAC-TTAATTCAGGGTAATTAAGT
21727 GAGTT
Statistics
Matches: 564, Mismatches: 37, Indels: 73
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.01
28 2 0.00
30 4 0.01
31 120 0.21
32 2 0.00
33 1 0.00
34 36 0.06
35 338 0.60
36 27 0.05
37 1 0.00
38 29 0.05
39 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (34 bp):
AACTTAATTCAGGGTAATTAAGTAATCAGTAATC
Done.