Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013462.1 Corchorus capsularis cultivar CVL-1 contig13483, 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: 20911
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Found at i:2838 original size:75 final size:74
Alignment explanation
Indices: 2711--2868 Score: 253
Period size: 75 Copynumber: 2.1 Consensus size: 74
2701 TGGTCTTTTC
* * * *
2711 ACACTTTTCGGGTGACTAAAAAGCCTCTCTATGAGTTTCCCCTATTCTTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
2776 TTCGTAATT
66 TTCGTAATT
*
2785 ACACTTTTTCGGATGTCTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
1 ACAC-TTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
2850 TTTCGTAATT
65 TTTCGTAATT
*
2860 ACACATTTC
1 ACACTTTTC
2869 TCTTCCTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 8 0.10
75 69 0.90
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.42
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:3946 original size:9 final size:9
Alignment explanation
Indices: 3932--3958 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3922 TTGAATTCTT
3932 TTTTTTTTA
1 TTTTTTTTA
3941 TTTTTTTTA
1 TTTTTTTTA
3950 TTTTTTTTA
1 TTTTTTTTA
3959 ACCTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:6184 original size:33 final size:33
Alignment explanation
Indices: 6087--6187 Score: 141
Period size: 33 Copynumber: 3.1 Consensus size: 33
6077 CTCTTACACC
* ** *
6087 CAATGAAGTT-GCGGGTTTTCATCACACCGTTA
1 CAATGAAGTTCACGGGCCTTCATCACACCTTTA
6119 CAATGAAGTTCACGGGCCTTCATCACACCTTTA
1 CAATGAAGTTCACGGGCCTTCATCACACCTTTA
**
6152 CAATGAAGTTCACGGGCCTTCATCACGTCTTTA
1 CAATGAAGTTCACGGGCCTTCATCACACCTTTA
6185 CAA
1 CAA
6188 GTTGAGCGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 10 0.16
33 52 0.84
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (33 bp):
CAATGAAGTTCACGGGCCTTCATCACACCTTTA
Found at i:7762 original size:12 final size:12
Alignment explanation
Indices: 7747--7792 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
7737 AATAAATAAT
7747 AATAATTTTTGA
1 AATAATTTTTGA
7759 AATAATTATTTTCGA
1 AATAA-T-TTTT-GA
*
7774 AATAATTTTCGA
1 AATAATTTTTGA
7786 AATAATT
1 AATAATT
7793 ATTATTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 14 0.47
13 4 0.13
14 5 0.17
15 7 0.23
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (12 bp):
AATAATTTTTGA
Found at i:7764 original size:15 final size:15
Alignment explanation
Indices: 7744--7791 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
7734 TTAAATAAAT
*
7744 AATAATAATTTTTGA
1 AATAATAATTTTCGA
*
7759 AATAATTATTTTCG-
1 AATAATAATTTTCGA
7773 -A-AATAATTTTCGA
1 AATAATAATTTTCGA
7786 AATAAT
1 AATAAT
7792 TATTATTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 1 0.04
15 15 0.56
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (15 bp):
AATAATAATTTTCGA
Found at i:8481 original size:20 final size:20
Alignment explanation
Indices: 8453--8491 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8443 AGTGCTTCAA
*
8453 ACACACTTCGACGGCTACAC
1 ACACACTTCGACAGCTACAC
* *
8473 ACACGCTTCTACAGCTACA
1 ACACACTTCGACAGCTACA
8492 AACTTGCTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (20 bp):
ACACACTTCGACAGCTACAC
Found at i:9700 original size:10 final size:10
Alignment explanation
Indices: 9685--9710 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9675 AGTTGCTGCC
9685 AAATTCCAGA
1 AAATTCCAGA
9695 AAATTCCAGA
1 AAATTCCAGA
9705 AAATTC
1 AAATTC
9711 TAGTCCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:9920 original size:21 final size:21
Alignment explanation
Indices: 9890--9950 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
9880 ACAGGTGACA
*
9890 GGCCATGCGACTTGGAGATCC
1 GGCCACGCGACTTGGAGATCC
9911 GGCCACGCGACTTGGAGATCC
1 GGCCACGCGACTTGGAGATCC
9932 GGCCACGCGACTTGGAGAT
1 GGCCACGCGACTTGGAGAT
9951 ACCCGCGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.30, G:0.34, T:0.16
Consensus pattern (21 bp):
GGCCACGCGACTTGGAGATCC
Found at i:9998 original size:33 final size:33
Alignment explanation
Indices: 9930--10010 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
9920 ACTTGGAGAT
*
9930 CCGGCCACGCGACTTGGAGATACCCGCGCAACA
1 CCGGCCACGCGACATGGAGATACCCGCGCAACA
* * * *
9963 CCGGCCATGTGACATGGAGATGCCCG-GCCATCA
1 CCGGCCACGCGACATGGAGATACCCGCG-CAACA
*
9996 CCGGCAACGCGACAT
1 CCGGCCACGCGACAT
10011 AGCCAAGCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 1 0.03
33 38 0.97
ACGTcount: A:0.23, C:0.37, G:0.28, T:0.11
Consensus pattern (33 bp):
CCGGCCACGCGACATGGAGATACCCGCGCAACA
Found at i:10990 original size:8 final size:8
Alignment explanation
Indices: 10977--11010 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
10967 CACCTTCTTG
10977 AAAAATTC
1 AAAAATTC
10985 AAAAATTC
1 AAAAATTC
*
10993 AGAAACTTC
1 A-AAAATTC
11002 AAAAATTC
1 AAAAATTC
11010 A
1 A
11011 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:11341 original size:20 final size:19
Alignment explanation
Indices: 11307--11347 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
11297 GGTTTTCATG
*
11307 TGCAATTGATCTAATTAAT
1 TGCAATTAATCTAATTAAT
*
11326 TGCAATTAACTCTAATTGAT
1 TGCAATTAA-TCTAATTAAT
11346 TG
1 TG
11348 TGTAATTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
TGCAATTAATCTAATTAAT
Found at i:16492 original size:21 final size:21
Alignment explanation
Indices: 16466--16507 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16456 GCACAAGTGA
*
16466 CCGGCCATGCGACTTAGAGAT
1 CCGGCCACGCGACTTAGAGAT
*
16487 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTAGAGAT
16508 GCCCGCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTAGAGAT
Found at i:16559 original size:33 final size:33
Alignment explanation
Indices: 16487--16593 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
16477 ACTTAGAGAT
*
16487 CCGGCCACGCGACTTGGAGATGCCCGCGCAACA
1 CCGGCCACGCGACATGGAGATGCCCGCGCAACA
* *
16520 CCGGCCATGCGACATGGAGATGCCCGAC-CATCA
1 CCGGCCACGCGACATGGAGATGCCCG-CGCAACA
* * ** *
16553 CTGGCCACGCGACATAGCCATGCCCG-GCCACA
1 CCGGCCACGCGACATGGAGATGCCCGCGCAACA
16585 CCCGGCCAC
1 -CCGGCCAC
16594 ATTACTCGGC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 3 0.05
33 56 0.93
34 1 0.02
ACGTcount: A:0.21, C:0.42, G:0.27, T:0.09
Consensus pattern (33 bp):
CCGGCCACGCGACATGGAGATGCCCGCGCAACA
Found at i:19753 original size:113 final size:106
Alignment explanation
Indices: 19558--19757 Score: 265
Period size: 106 Copynumber: 1.8 Consensus size: 106
19548 AGATATTTTG
* * *
19558 GTCAAATTTGCCACTCCTTTCACGTGCTAACCCTATTGCATGGTGGGTCTCCTACATCTTTTAAC
1 GTCAAATTGGCCACTCCTTTCACGTGCTAACCCTATTGCATGGTGGGTCCCCTACATCTTTCAAC
*
19623 AGTGTTATCACGTATTGAACCGTTCGGACGACTTAACCGGT
66 AGTGTTATCACATATTGAACCGTTCGGACGACTTAACCGGT
* * *
19664 GTCAAATTGGCCTCTCTTTTCACGTGCTAAGCCTATTGCATGGTGGTTGGTGGATCCCCTACATC
1 GTCAAATTGGCCACTCCTTTCACGTGCTAACCCTATTGCA---TGG-T-G-GG-TCCCCTACATC
*
19729 TTTCAACAGTTTTATCACATATTGAACCG
59 TTTCAACAGTGTTATCACATATTGAACCG
19758 CTCGATGGCT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
106 36 0.46
109 3 0.04
110 1 0.01
111 1 0.01
112 2 0.03
113 36 0.46
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (106 bp):
GTCAAATTGGCCACTCCTTTCACGTGCTAACCCTATTGCATGGTGGGTCCCCTACATCTTTCAAC
AGTGTTATCACATATTGAACCGTTCGGACGACTTAACCGGT
Done.