Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018720.1 Corchorus olitorius cultivar O-4 contig18753, 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: 4695
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Found at i:203 original size:15 final size:15
Alignment explanation
Indices: 145--204 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
135 GGGTTGGTAT
*
145 GGCATAGGTGGCAAC
1 GGCATAGGTGGAAAC
* * *
160 GGCATACGCGGATAC
1 GGCATAGGTGGAAAC
* *
175 GGCAAAGGTTGAAAC
1 GGCATAGGTGGAAAC
*
190 GCCATAGGTGGAAAC
1 GGCATAGGTGGAAAC
205 ATCATTGGCG
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13
Consensus pattern (15 bp):
GGCATAGGTGGAAAC
Found at i:1670 original size:13 final size:13
Alignment explanation
Indices: 1637--1689 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
1627 GCACCCAAAA
*
1637 CATTTAT-TAAAA
1 CATTTATATAAAG
1649 CATTT-TATAAAG
1 CATTTATATAAAG
1661 CATTTATATAAAG
1 CATTTATATAAAG
*
1674 CAGTTATA-AAA-
1 CATTTATATAAAG
1685 CATTT
1 CATTT
1690 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:2117 original size:27 final size:28
Alignment explanation
Indices: 2087--2149 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
2077 TCCGACGTTT
* *
2087 AAGGGCAAAATTGTAA-TTTAGTCAACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
* *
2114 AA-GGTAAAATGGTAATTTTAGCCGACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
2141 AAGGGCAAA
1 AAGGGCAAA
2150 TACGTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 11 0.38
27 13 0.45
28 5 0.17
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (28 bp):
AAGGGCAAAATGGTAATTTTAGCCAACC
Found at i:2150 original size:27 final size:27
Alignment explanation
Indices: 2087--2161 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
2077 TCCGACGTTT
* *
2087 AAGGGCAAAATTGTAA-TTTAGTCAACC
1 AAGGGC-AAATCGTAATTTTAGCCAACC
** * *
2114 AAGGTAAAATGGTAATTTTAGCCGACC
1 AAGGGCAAATCGTAATTTTAGCCAACC
2141 AAGGGCAAATACGTAATTTTA
1 AAGGGCAAAT-CGTAATTTTA
2162 ACATCCTAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 8 0.21
27 21 0.55
28 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (27 bp):
AAGGGCAAATCGTAATTTTAGCCAACC
Found at i:2967 original size:34 final size:33
Alignment explanation
Indices: 2929--3007 Score: 79
Period size: 34 Copynumber: 2.3 Consensus size: 33
2919 TTTTATTTCC
2929 TTTTCT-TCCCTTATCCGGTTTTCCCTTTTCTTTT
1 TTTTCTCTCCCTTATCC--TTTTCCCTTTTCTTTT
* * *
2963 TTTTCCTCTTCCTTTTCCTTTTCCTTTTTCTTTT
1 TTTT-CTCTCCCTTATCCTTTTCCCTTTTCTTTT
2997 TCTTTCCTCTC
1 T-TTT-CTCTC
3008 TTTTCCTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
34 20 0.53
35 10 0.26
36 8 0.21
ACGTcount: A:0.01, C:0.32, G:0.03, T:0.65
Consensus pattern (33 bp):
TTTTCTCTCCCTTATCCTTTTCCCTTTTCTTTT
Found at i:2974 original size:6 final size:6
Alignment explanation
Indices: 2947--3001 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
2937 CCTTATCCGG
* *
2947 TTTTCCC TTTT-C TTTT-- TTTTCC TCTTCC TTTTCC TTTTCC TTTTTC
1 TTTT-CC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC
*
2993 TTTTTC TTT
1 TTTTCC TTT
3002 CCTCTCTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
4 4 0.09
5 5 0.12
6 30 0.70
7 4 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTCC
Found at i:2986 original size:18 final size:17
Alignment explanation
Indices: 2963--3014 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
2953 CTTTTCTTTT
2963 TTTTCCTCTTCCTTTTCC
1 TTTTCCTCTT-CTTTTCC
* *
2981 TTTTCCTTTTTCTTTTTC
1 TTTTCC-TCTTCTTTTCC
2999 -TTTCCTC-TCTTTTCC
1 TTTTCCTCTTCTTTTCC
3014 T
1 T
3015 GGCTTGGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 7 0.25
16 1 0.04
17 5 0.18
18 12 0.43
19 3 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTCCTCTTCTTTTCC
Found at i:2997 original size:33 final size:33
Alignment explanation
Indices: 2947--3014 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 33
2937 CCTTATCCGG
2947 TTTTCCCTTTTCTTTTT-TTTCCTCTTCCTTTTCC
1 TTTTCCCTTTTCTTTTTCTTTCCTC-T-CTTTTCC
*
2981 TTTTCCTTTTTCTTTTTCTTTCCTCTCTTTTCC
1 TTTTCCCTTTTCTTTTTCTTTCCTCTCTTTTCC
3014 T
1 T
3015 GGCTTGGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 8 0.25
34 17 0.53
35 7 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (33 bp):
TTTTCCCTTTTCTTTTTCTTTCCTCTCTTTTCC
Done.