Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024104.1 Corchorus olitorius cultivar O-4 contig24137, 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: 8829
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Found at i:905 original size:26 final size:24
Alignment explanation
Indices: 871--935 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 24
861 ATGGCTTTTT
871 TTTTC-CTTTTCTTTTTTATTTCTC
1 TTTTCTCTTTTCTTTTTT-TTTCTC
*
895 TTTTCTTCTTTTACTTTTTTTTTCTT
1 TTTTC-TCTTTT-CTTTTTTTTTCTC
921 TTTTCTCTTCTTCTT
1 TTTTCTCTT-TTCTT
936 CTTTCTCAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 5 0.14
25 7 0.19
26 17 0.47
27 7 0.19
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCTCTTTTCTTTTTTTTTCTC
Found at i:932 original size:31 final size:32
Alignment explanation
Indices: 871--939 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
861 ATGGCTTTTT
* *
871 TTTTCCTTTTCTTTTTTATTTCTCTTTTCTTC
1 TTTTACTTTTCTTTTTTATTTCTCTCTTCTTC
* *
903 TTTTACTTTTTTTTTCTTTTTTCTCTTCTTCTTC
1 TTTTACTTTTCTTTT-TTATTTCTC-TCTTCTTC
937 TTT
1 TTT
940 CTCAACCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 13 0.42
33 8 0.26
34 10 0.32
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTTACTTTTCTTTTTTATTTCTCTCTTCTTC
Found at i:6403 original size:35 final size:35
Alignment explanation
Indices: 6321--6695 Score: 261
Period size: 35 Copynumber: 10.8 Consensus size: 35
6311 TTCAATTAAC
* * * * ** *
6321 CCAGGGCGATCCTTTATTCAGTTTACTTCAGCAGAC
1 CCAGGGCGGT-CTTTCTTCAATTTATTTCAGTTGAT
* *
6357 CCAGGGCGGTCTTTCTCCAATTTATTTTAGTTGAT
1 CCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGAT
* *
6392 CCAGGGCGGTCTTTCTTCCATTTATTTTAGTTGAT
1 CCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGAT
* * * * *
6427 CCAGGGCGATCTTTTTTTTCAATTCACTCCAGTTGAT
1 CCAGGGCGGTC--TTTCTTCAATTTATTTCAGTTGAT
* * * * *
6464 CCAAGGCGATCCTTCCTTTAGTTTATTTCAGTTGA-
1 CCAGGGCGGT-CTTTCTTCAATTTATTTCAGTTGAT
* *
6499 CACAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAC
1 C-CAGGGCGGTCTTTCTTCAATTTATTTCAGTTGAT
* *
6535 CCAGGGCGGTCTTTCTTTAATTTATTTCTGTTGAT
1 CCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGAT
* *
6570 CCAGGGCGATCTTTCCTT-AGTTTATTTCAGTTGAT
1 CCAGGGCGGTCTTT-CTTCAATTTATTTCAGTTGAT
** * * *
6605 TGAGGGTGATC-TT-TTC--TTTA----A-TTAAT
1 CCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGAT
* *
6631 CCAGGGCGATCTTTCTTCAATTTACTTT-AGTAGAT
1 CCAGGGCGGTCTTTCTTCAATTTA-TTTCAGTTGAT
* * *
6666 CCAGGGCGATCTTCTCTGCAGTTTATTTCA
1 CCAGGGCGGTCTT-TCTTCAATTTATTTCA
6696 ATCGCCTGTA
Statistics
Matches: 273, Mismatches: 48, Indels: 36
0.76 0.13 0.10
Matches are distributed among these distances:
26 12 0.04
27 3 0.01
28 3 0.01
30 4 0.01
31 4 0.01
32 2 0.01
34 3 0.01
35 168 0.62
36 46 0.17
37 27 0.10
38 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
CCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGAT
Found at i:6514 original size:108 final size:105
Alignment explanation
Indices: 6377--6604 Score: 298
Period size: 108 Copynumber: 2.1 Consensus size: 105
6367 CTTTCTCCAA
* * *
6377 TTTATTTTAGTTGATCCAGGGCGGTCTTTCTTCCA-TTTATTTTAGTTGATCCAGGGCGATCTTT
1 TTTATTTCAGTTGATCCAGGGCGGTCTTTCTT-CAGTTTATTTCAGTTGACCCAGGGCGATC-TT
*
6441 TTTTTCAATTCACTCCAGTTGATCCAAGGCGATCCTTCCTTTAG
64 TCTTT-AATTCACTCCAGTTGATCCAAGGCGATCCTTCC-TTAG
*
6485 TTTATTTCAGTTGA-CACAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
1 TTTATTTCAGTTGATC-CAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTT
* * * * * *
6549 CTTTAATTTATTTCTGTTGATCCAGGGCGATCTTTCCTTAG
65 CTTTAATTCACTCCAGTTGATCCAAGGCGATCCTTCCTTAG
6590 TTTATTTCAGTTGAT
1 TTTATTTCAGTTGAT
6605 TGAGGGTGAT
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
105 18 0.17
106 27 0.25
107 9 0.08
108 52 0.49
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (105 bp):
TTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTC
TTTAATTCACTCCAGTTGATCCAAGGCGATCCTTCCTTAG
Found at i:6583 original size:143 final size:143
Alignment explanation
Indices: 6325--6583 Score: 385
Period size: 143 Copynumber: 1.8 Consensus size: 143
6315 ATTAACCCAG
* * *
6325 GGCGATCCTTTATTCAGTTTACTTCAGCAGACCCAGGGCGGTCTTTCTCCAATTTATTTTAGTTG
1 GGCGATCCTTCATTCAGTTTACTTCAGCAGACACAGGGCGGTCTTTCTCCAATTTATTTCAGTTG
* *
6390 ATCCAGGGCGGTCTTTCTTCCATTTATTTTAGTTGATCCAGGGCGATCTTTTTTTTCAATTCACT
66 ACCCAGGGCGGTCTTTCTTCAATTTATTTTAGTTGATCCAGGGCGATCTTTTTTTTCAATTCACT
6455 CCAGTTGATCCAA
131 CCAGTTGATCCAA
* * * ** * *
6468 GGCGATCCTTCCTTTAGTTTATTTCAGTTGACACAGGGCGGTCTTTCTTCAGTTTATTTCAGTTG
1 GGCGATCCTTCATTCAGTTTACTTCAGCAGACACAGGGCGGTCTTTCTCCAATTTATTTCAGTTG
*
6533 ACCCAGGGCGGTCTTTCTTTAATTTATTTCT-GTTGATCCAGGGCGATCTTT
66 ACCCAGGGCGGTCTTTCTTCAATTTATTT-TAGTTGATCCAGGGCGATCTTT
6584 CCTTAGTTTA
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
143 101 0.99
144 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (143 bp):
GGCGATCCTTCATTCAGTTTACTTCAGCAGACACAGGGCGGTCTTTCTCCAATTTATTTCAGTTG
ACCCAGGGCGGTCTTTCTTCAATTTATTTTAGTTGATCCAGGGCGATCTTTTTTTTCAATTCACT
CCAGTTGATCCAA
Found at i:7000 original size:30 final size:30
Alignment explanation
Indices: 6966--7834 Score: 1008
Period size: 30 Copynumber: 28.9 Consensus size: 30
6956 TTTATCGTCG
6966 TTATTTTAATCCTGGTTGAGGAT-ACTTGCT
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
*
6996 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
* * * * *
7026 TTGTGTTCAATCCTGTTTGAGGGTCATCGCT
1 TTAT-TTTAATCCTGGTTGAGGATCATTGCT
* * *
7057 TTATTTTAATCATGTTTGATGATCATTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
** * *
7087 TCGTTTTAATCCTGTTTGAGGATCATCGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
*
7117 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
* * *
7147 TCATTTTAACCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
7177 TTATTTTAATCCTGGTTGAGGAT-ATTTGCT
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
* *
7207 TTATTTTAATCCTAGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
* *
7237 TTATTTTAATCTTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
*
7267 TTATTTTAATCCTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
**
7297 TTATTTTAATCCTGGTTGAGGATGTTTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
* *
7327 TCATTTTAATCCTGGTTGAGGATCGTTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
**
7357 TTATTTTAATCCTGGTTGAGGATGTTTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
*
7387 TCATTTTAATCCTGGTTGAGGAT-ATTTGCT
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
**
7417 TTATTTTAATCCTAATTGAGGAT-ATTTGCT
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
*
7447 TTATTTTAATCCTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
*
7477 TTATTTTAATCCTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
7507 TTATTTTAATCCTGGTTGAGGAT-ATTTGCT
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
* * *
7537 TAATTTTAATCCTGGTTGAGGACCGTTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
*
7567 TTATTTTAAT-CTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
*
7596 TTATTTTAATCCTGGTTGAGGAT-ATTTGCC
1 TTATTTTAATCCTGGTTGAGGATCA-TTGCT
* * * *
7626 TTACTTTAAATCCTGTTTGAGGGTCTTTGCT
1 TTA-TTTTAATCCTGGTTGAGGATCATTGCT
* * * * *
7657 TTGTTTCACTCCTGTTTGAGGATCGTTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
* * *
7687 TCATTTTAATCCTGTTTGAGGATCTTTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
* *
7717 TTGTTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
*
7747 TTATTTTAATCCTGGTTGAGGATCATAGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
*
7777 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGGTTGAGGATCATTGCT
* * *
7807 TTGTTTTAATCTTGGTTTAGGATCATTG
1 TTATTTTAATCCTGGTTGAGGATCATTG
7835 TTTCGTCAGT
Statistics
Matches: 749, Mismatches: 80, Indels: 20
0.88 0.09 0.02
Matches are distributed among these distances:
29 26 0.03
30 673 0.90
31 50 0.07
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.48
Consensus pattern (30 bp):
TTATTTTAATCCTGGTTGAGGATCATTGCT
Found at i:8434 original size:27 final size:27
Alignment explanation
Indices: 8367--8434 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
8357 CTAGGGGGGT
* * *
8367 ATTTTGGTAATTTGCACATTCAGGGGC
1 ATTTTGGTCATTTTCACATTCAAGGGC
*
8394 ATTTTGGTCATTTTTACATTCAAGGGC
1 ATTTTGGTCATTTTCACATTCAAGGGC
8421 ATTTTGGTCATTTT
1 ATTTTGGTCATTTT
8435 GGTCATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (27 bp):
ATTTTGGTCATTTTCACATTCAAGGGC
Done.