Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009374.1 Corchorus capsularis cultivar CVL-1 contig09395, 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: 12049
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Found at i:3876 original size:17 final size:17
Alignment explanation
Indices: 3856--3888 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3846 GGTTAGGTTT
3856 GGGTTCAAATTCAGATC
1 GGGTTCAAATTCAGATC
3873 GGGTTCAAATTCAGAT
1 GGGTTCAAATTCAGAT
3889 AGTTAACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (17 bp):
GGGTTCAAATTCAGATC
Found at i:4024 original size:3 final size:3
Alignment explanation
Indices: 4016--4087 Score: 108
Period size: 3 Copynumber: 23.3 Consensus size: 3
4006 AAAATTTCCC
4016 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4064 TAT TAC TAT ATAC TAT ATAT TAT T
1 TAT TAT TAT -TAT TAT -TAT TAT T
4088 TTTAGTGACT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
3 58 0.92
4 5 0.08
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:6234 original size:3 final size:3
Alignment explanation
Indices: 6228--6265 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
6218 GTTGTTGTTC
6228 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6266 ATATATGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6259 original size:25 final size:25
Alignment explanation
Indices: 6228--6308 Score: 56
Period size: 29 Copynumber: 3.0 Consensus size: 25
6218 GTTGTTGTTC
6228 TTATTATATATTAT-TATTATTATTA
1 TTATTATATA-TATGTATTATTATTA
* *
6253 TTATTATTATTATATATATGTATTCATTTTC
1 TTATTA-TA-TATATGTAT-TATT-A--TTA
* *
6284 TTAGTATATATATGTATTGTTATTA
1 TTATTATATATATGTATTATTATTA
6309 AAAATGGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
25 8 0.18
26 5 0.11
27 6 0.14
28 7 0.16
29 9 0.20
30 2 0.05
31 7 0.16
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.60
Consensus pattern (25 bp):
TTATTATATATATGTATTATTATTA
Found at i:8715 original size:126 final size:126
Alignment explanation
Indices: 8533--8760 Score: 384
Period size: 126 Copynumber: 1.8 Consensus size: 126
8523 GGACGAGGTC
*
8533 GATTCATGTCGATCGCCAATTAATCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
1 GATTCAAGTCGATCGCCAATTAATCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
* *
8598 CGCCTGTTGGCGTTGGGCCCCTTGTGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
66 CGCCTGTTGACGTTGGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
* ** *
8659 GATTCAAGTCGATCGCCACTTTGTCGGTGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
1 GATTCAAGTCGATCGCCAATTAATCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
*
8724 CGCCTGTTGACGTTGGGCCCCTTGAGGGCATTATCAT
66 CGCCTGTTGACGTTGGGCCCCTTGAGGGCATCATCAT
8761 TTCCCCGACT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 94 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (126 bp):
GATTCAAGTCGATCGCCAATTAATCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
CGCCTGTTGACGTTGGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
Found at i:10837 original size:26 final size:26
Alignment explanation
Indices: 10808--10929 Score: 140
Period size: 26 Copynumber: 4.7 Consensus size: 26
10798 TCGCACGCGC
10808 GAGGTCACGTGTGGAGTTGTAC-TTAG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * *
10834 GAGGTCACGTGTTGAAGGTGTCCGTTG
1 GAGGTCACGTG-TGGAGTTGTACGTTG
*
10861 GAGGTCACGTATGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * *
10887 GAGATCACGTTTGGAGTCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACGTTG
10913 GAGGTCACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
10930 GCCAGTTGGC
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.03
26 55 0.69
27 21 0.26
28 2 0.03
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (26 bp):
GAGGTCACGTGTGGAGTTGTACGTTG
Found at i:10895 original size:53 final size:52
Alignment explanation
Indices: 10808--10929 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 52
10798 TCGCACGCGC
* *
10808 GAGGTCACGTGTGGAGTTGTACTTAGGAGGTCACGTGTTGAAGGT-GTCCGTTG
1 GAGGTCACGTGTGGAGTTGTACTTAGGAGATCACGT-TTGAA-GTCGTACGTTG
* * *
10861 GAGGTCACGTATGGAGTTGTACTTCGGAGATCACGTTTGGAGTCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACTTAGGAGATCACGTTTGAAGTCGTACGTTG
10913 GAGGTCACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
10930 GCCAGTTGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 27 0.44
53 33 0.53
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (52 bp):
GAGGTCACGTGTGGAGTTGTACTTAGGAGATCACGTTTGAAGTCGTACGTTG
Found at i:10990 original size:15 final size:15
Alignment explanation
Indices: 10970--10999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10960 TTGTGGTCAT
10970 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
*
10985 AGGTGGTCGGGCGCC
1 AGGTGGTCGAGCGCC
11000 GGGCTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.50, T:0.13
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Done.