Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016499.1 Corchorus olitorius cultivar O-4 contig16532, 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: 19245
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:4983 original size:261 final size:261
Alignment explanation
Indices: 4519--5041 Score: 940
Period size: 261 Copynumber: 2.0 Consensus size: 261
4509 CAGTCTAATG
* *
4519 AGGTCCAAAGCTTGGTGAGGGACCCACTAAACCTATAGGTCCAGTCTTGTCACCTGAATCTAGGT
1 AGGTCCAAAGCTTGGCGAGGGACCCACTAAACCTATAGATCCAGTCTTGTCACCTGAATCTAGGT
* * *
4584 TCGGGAGTCGATTATTCCCGGGGAAGGATGAGCACCCTTGGAACGCCCGTCAAAAGACAGTACCT
66 TCGGGAGTCGATTATGCCCGGGGAAGGATGAGCACCCTCGGAACGCCCGTCAAAAAACAGTACCT
* * *
4649 CTGAGTCTAATTAGATGTAATGTGGGTCTAAAATAAAAAGGTTGTTTTTAGTCCTTAGTCCTATA
131 CTAAGTCTAACTAGATGTAATGTGGGTCTAAAATAAAAAGGTTGCTTTTAGTCCTTAGTCCTATA
4714 TTTTTAGTTTTTTCTTGTTTCAAGGGAATTGAAACCTTTTATTACTCATGAAAATATGACAAAAC
196 TTTTTAGTTTTTTCTTGTTTCAAGGGAATTGAAACCTTTTATTACTCATGAAAATATGACAAAAC
4779 A
261 A
4780 AGGTCCAAAGCTTGGCGAGGGACCCACTAAACCTATAGATCCAGTCTTGTCACCTGAATCTAGGT
1 AGGTCCAAAGCTTGGCGAGGGACCCACTAAACCTATAGATCCAGTCTTGTCACCTGAATCTAGGT
*
4845 TCGGGAGTCGATTATGCCCGGGGAAGGATGAGCACACC-CGGAACGCCCGTCAAAAAACGGTACC
66 TCGGGAGTCGATTATGCCCGGGGAAGGATGAGCAC-CCTCGGAACGCCCGTCAAAAAACAGTACC
4909 TCTAAGTCTAACTAGATGTAATGTGGGTCTAAAATAAAAAGGTTGCTTTTAGTCCTTAGTCCTAT
130 TCTAAGTCTAACTAGATGTAATGTGGGTCTAAAATAAAAAGGTTGCTTTTAGTCCTTAGTCCTAT
*
4974 ATTTTTAGTTTTTTCTTGTTTCAAGGGAATTGAAACCTTTTATTACTCGTGAAAATATGACAAAA
195 ATTTTTAGTTTTTTCTTGTTTCAAGGGAATTGAAACCTTTTATTACTCATGAAAATATGACAAAA
5039 CA
260 CA
5041 A
1 A
5042 TGCCTTCCGA
Statistics
Matches: 251, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
261 249 0.99
262 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (261 bp):
AGGTCCAAAGCTTGGCGAGGGACCCACTAAACCTATAGATCCAGTCTTGTCACCTGAATCTAGGT
TCGGGAGTCGATTATGCCCGGGGAAGGATGAGCACCCTCGGAACGCCCGTCAAAAAACAGTACCT
CTAAGTCTAACTAGATGTAATGTGGGTCTAAAATAAAAAGGTTGCTTTTAGTCCTTAGTCCTATA
TTTTTAGTTTTTTCTTGTTTCAAGGGAATTGAAACCTTTTATTACTCATGAAAATATGACAAAAC
A
Found at i:6133 original size:27 final size:28
Alignment explanation
Indices: 6100--6177 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
6090 AATTTTTGTG
6100 TTTTGCGTTTTTGAAAAAAAAA-AGAGT
1 TTTTGCGTTTTTGAAAAAAAAACAGAGT
* ***
6127 TTTTGCGTCTTCT-AAAAAAAAACTTTGT
1 TTTTGCGT-TTTTGAAAAAAAAACAGAGT
*
6155 TTCTGCGTTTTTAGAAAAAAAAA
1 TTTTGCGTTTTT-GAAAAAAAAA
6178 TATTTTTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
27 20 0.49
28 12 0.29
29 9 0.22
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (28 bp):
TTTTGCGTTTTTGAAAAAAAAACAGAGT
Found at i:6185 original size:28 final size:28
Alignment explanation
Indices: 6103--6186 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
6093 TTTTGTGTTT
* *
6103 TGCGTTTTT-GAAAAAAAAAAGAGTTTT-
1 TGCGTTTTTAG-AAAAAAAAATATTTTTC
* *
6130 TGCGTCTTCTA-AAAAAAAACT-TTGTTTC
1 TGCGT-TTTTAGAAAAAAAAATATT-TTTC
6158 TGCGTTTTTAGAAAAAAAAATATTTTTC
1 TGCGTTTTTAGAAAAAAAAATATTTTTC
6186 T
1 T
6187 TTATTTTCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
26 1 0.02
27 20 0.44
28 22 0.49
29 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (28 bp):
TGCGTTTTTAGAAAAAAAAATATTTTTC
Found at i:8652 original size:19 final size:19
Alignment explanation
Indices: 8630--8666 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8620 GAGAGGAAGG
* *
8630 AAGAGAATAAAATAAGAAA
1 AAGAGAAAAAAAGAAGAAA
8649 AAGAGAAAAAAAGAAGAA
1 AAGAGAAAAAAAGAAGAA
8667 CTAAGGTCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
AAGAGAAAAAAAGAAGAAA
Found at i:17616 original size:14 final size:14
Alignment explanation
Indices: 17597--17625 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17587 ATTGATGATG
17597 ATTCATACTACCAA
1 ATTCATACTACCAA
17611 ATTCATACTACCAA
1 ATTCATACTACCAA
17625 A
1 A
17626 AGTTTCCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTCATACTACCAA
Done.