Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015220.1 Corchorus olitorius cultivar O-4 contig15253, 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: 7775
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:5980 original size:36 final size:36
Alignment explanation
Indices: 5784--6472 Score: 748
Period size: 36 Copynumber: 19.6 Consensus size: 36
5774 ATTTCAGATG
* * * *
5784 CTTCAGTTCATTTCAGTTGACCCAAGGCGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * *
5819 ATTCAGTTTATTTCAGCTGACCCAGGGCGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
5854 CTTTAATTCACTTCAGTTGATCCAGGGCGATC-CTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * * * * *
5889 GTTCAATTCATTTCAGTTGACCCAGGGTGGTCATAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
5925 -TTCAGTTTATTTCAGTTGATCTAGGGCGATCCTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * **
5960 CTTCAGTTTATATAAATTGATCCAGGGCGATCCTCC
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
5996 CTTCAGTTTATTTCAGTTGA-CCTAGGGCGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCC-AGGGCGATCTTTT
6031 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6067 CTTCAGTTTATCTCAATTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6103 CTTCAGTTTATCTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * **
6139 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTCC
1 CTTCAGTTTAT-TTCAGTTGATCCAGGGCGATCTTTT
*
6175 CTTCAGTTTATTTTAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
6211 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
6247 CTTTAGTTTATTTCAATTGATCTAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6283 CTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
6319 CTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6355 CTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
6391 C--C---TTA----A-TTGATCCAGGGCGAT-TTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
6416 CCTCAATTTACTTCAGTAGATCCAGGGCGATCTTCT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
6452 CTGCAATTTATTTCAATTGAT
1 CTTCAGTTTATTTCAGTTGAT
6473 TGCAAAATGG
Statistics
Matches: 562, Mismatches: 74, Indels: 35
0.84 0.11 0.05
Matches are distributed among these distances:
25 5 0.01
26 14 0.02
27 2 0.00
30 3 0.01
31 3 0.01
34 2 0.00
35 157 0.28
36 375 0.67
37 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (36 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:6423 original size:25 final size:26
Alignment explanation
Indices: 6371--6423 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
6361 TTTATTTCAG
* *
6371 TTGATCGAGGGCGATCTTTTCCTTAA
1 TTGATCCAGGGCGATCTTTTCCTCAA
6397 TTGATCCAGGGCGAT-TTTTCCTCAA
1 TTGATCCAGGGCGATCTTTTCCTCAA
6422 TT
1 TT
6424 TACTTCAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (26 bp):
TTGATCCAGGGCGATCTTTTCCTCAA
Found at i:6432 original size:61 final size:62
Alignment explanation
Indices: 6333--6449 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 62
6323 AGTTTATTTC
* * * * * *
6333 AATTGATCCGGGGCAATCTTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTTCCTT
1 AATTGATCCAGGGCAATCTTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTTTTCCTT
*
6395 AATTGATCCAGGGCGAT-TTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTT
1 AATTGATCCAGGGCAATCTTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTT
6450 CTCTGCAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 33 0.69
62 15 0.31
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (62 bp):
AATTGATCCAGGGCAATCTTTTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTTTTCCTT
Found at i:6769 original size:30 final size:30
Alignment explanation
Indices: 6734--6927 Score: 248
Period size: 30 Copynumber: 6.5 Consensus size: 30
6724 TGCTTTATCA
* *
6734 GCTTTATTTCAATCCTGGTTGAGGATATTT
1 GCTTTATTTTAATCCTGGTTGAGGATAGTT
* * *
6764 TCTTTATTTTAATCCTGTTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAGTT
6794 GCTTTATTTTAATCCTGGTTGAGGATCA-TT
1 GCTTTATTTTAATCCTGGTTGAGGAT-AGTT
* * *
6824 GCTTTATTTTAATCATGTTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATAGTT
*
6854 GCTTTATTTTAATCCTGGTTGAGGATAATT
1 GCTTTATTTTAATCCTGGTTGAGGATAGTT
* *
6884 GCTTTATTTTAATCCTGGTTTAGGATCA-TC
1 GCTTTATTTTAATCCTGGTTGAGGAT-AGTT
*
6914 ACTTTATTTTAATC
1 GCTTTATTTTAATC
6928 GAATCTTGTT
Statistics
Matches: 143, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
30 142 0.99
31 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (30 bp):
GCTTTATTTTAATCCTGGTTGAGGATAGTT
Found at i:6800 original size:60 final size:59
Alignment explanation
Indices: 6734--6927 Score: 291
Period size: 60 Copynumber: 3.2 Consensus size: 59
6724 TGCTTTATCA
* *
6734 GCTTTATTTCAATCCTGGTTGAGGATATTTTCTTTATTTTAATCCTGTTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGATA-TTGCTTTATTTTAATCCTGTTTGAGGATCGTT
*
6794 GCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCATGTTTGAGGATCGTT
1 GCTTTATTTTAATCCTGGTTGAGGAT-ATTGCTTTATTTTAATCCTGTTTGAGGATCGTT
* *
6854 GCTTTATTTTAATCCTGGTTGAGGATAATTGCTTTATTTTAATCCTGGTTT-AGGATCATC
1 GCTTTATTTTAATCCTGGTTGAGGAT-ATTGCTTTATTTTAATCCT-GTTTGAGGATCGTT
*
6914 ACTTTATTTTAATC
1 GCTTTATTTTAATC
6928 GAATCTTGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
60 119 0.96
61 5 0.04
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (59 bp):
GCTTTATTTTAATCCTGGTTGAGGATATTGCTTTATTTTAATCCTGTTTGAGGATCGTT
Found at i:6846 original size:90 final size:90
Alignment explanation
Indices: 6734--6927 Score: 280
Period size: 90 Copynumber: 2.2 Consensus size: 90
6724 TGCTTTATCA
* * * * * **
6734 GCTTTATTTCAATCCTGGTTGAGGATATTTTCTTTATTTTAATCCTGTTTGAGGATCGTTGCTTT
1 GCTTTATTTTAATCATGGTTGAGGATAGTTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTTT
*
6799 ATTTTAATCCTGGTTGAGGATCATT
66 ATTTTAATCCTGGTTGAGGATCATC
* *
6824 GCTTTATTTTAATCATGTTTGAGGATCGTTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTTT
1 GCTTTATTTTAATCATGGTTGAGGATAGTTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTTT
*
6889 ATTTTAATCCTGGTTTAGGATCATC
66 ATTTTAATCCTGGTTGAGGATCATC
*
6914 ACTTTATTTTAATC
1 GCTTTATTTTAATC
6928 GAATCTTGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (90 bp):
GCTTTATTTTAATCATGGTTGAGGATAGTTGCTTTATTTTAATCCTGGTTGAGGATAATTGCTTT
ATTTTAATCCTGGTTGAGGATCATC
Found at i:7390 original size:28 final size:27
Alignment explanation
Indices: 7358--7437 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 27
7348 GCACTTAGGT
7358 CATTTAGGGGCATTTTGGTCATTTTTC
1 CATTTAGGGGCATTTTGGTCATTTTTC
*
7385 ACATTTAGGGGCATTTTGGT--TATTTC
1 -CATTTAGGGGCATTTTGGTCATTTTTC
7411 CATGTTCAGGGGCATTTTGGTCATTTT
1 CAT-TT-AGGGGCATTTTGGTCATTTT
7438 AGGTTCATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
25 3 0.07
26 7 0.15
27 14 0.30
28 19 0.41
29 3 0.07
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (27 bp):
CATTTAGGGGCATTTTGGTCATTTTTC
Done.