Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023715.1 Corchorus olitorius cultivar O-4 contig23748, 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: 22644
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:341 original size:16 final size:16
Alignment explanation
Indices: 320--354 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
310 TATGGTTAAA
*
320 TTAAATGAATTTAATT
1 TTAAATAAATTTAATT
336 TTAAATAAATTTAATT
1 TTAAATAAATTTAATT
352 TTA
1 TTA
355 TTTCAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAAATAAATTTAATT
Found at i:2886 original size:27 final size:27
Alignment explanation
Indices: 2851--2963 Score: 163
Period size: 27 Copynumber: 4.2 Consensus size: 27
2841 ATTAGCTAAT
* *
2851 CTAACCATGCAAATGACTAAAATGCCC
1 CTAAACATGCAAATGACTAAAATACCC
*
2878 CTGAACATGCAAATGACTAAAATACCC
1 CTAAACATGCAAATGACTAAAATACCC
*
2905 CTAAACGTGCAAATGACTAAAATACCC
1 CTAAACATGCAAATGACTAAAATACCC
* * *
2932 TTAAACATGTAAATGACTAAAATGCCC
1 CTAAACATGCAAATGACTAAAATACCC
2959 CTAAA
1 CTAAA
2964 TGACCCTGAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.20
Consensus pattern (27 bp):
CTAAACATGCAAATGACTAAAATACCC
Found at i:9131 original size:21 final size:23
Alignment explanation
Indices: 9098--9142 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
9088 TATTATTTTT
9098 TTTGCGTTTTTGAAA-AAAAAAA
1 TTTGCGTTTTTGAAATAAAAAAA
9120 TTTGCG-TTTTGAAATTAAAAAAA
1 TTTGCGTTTTTGAAA-TAAAAAAA
9143 AAATCTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (23 bp):
TTTGCGTTTTTGAAATAAAAAAA
Found at i:16810 original size:19 final size:18
Alignment explanation
Indices: 16786--16821 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16776 TGAAAACTCA
16786 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
16805 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
16822 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:19883 original size:16 final size:16
Alignment explanation
Indices: 19862--19897 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19852 CTTGCTTCAG
*
19862 GTCGTCAAAGGAAGTC
1 GTCGTCAAACGAAGTC
*
19878 GTCGTCAAACGAGGTC
1 GTCGTCAAACGAAGTC
19894 GTCG
1 GTCG
19898 AAGGACGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.19
Consensus pattern (16 bp):
GTCGTCAAACGAAGTC
Found at i:22165 original size:29 final size:29
Alignment explanation
Indices: 22134--22283 Score: 147
Period size: 29 Copynumber: 5.1 Consensus size: 29
22124 TTAATTGACA
*
22134 TTTTGCAAATCTTGGGGGCATTTTGGTCAT
1 TTTTGCAAATC-CGGGGGCATTTTGGTCAT
* ** * **
22164 TTTTACCCATCCAGGGGTGTTTTGGTCAT
1 TTTTGCAAATCCGGGGGCATTTTGGTCAT
* *
22193 TTTTGCATATCCGGGGGTATTTTGGTCAT
1 TTTTGCAAATCCGGGGGCATTTTGGTCAT
* ** ** *
22222 TTTTACCCATCCAAGGGCATTTTAGTCAT
1 TTTTGCAAATCCGGGGGCATTTTGGTCAT
22251 TTTTGCACAATCCGGGGGCATTTTGGTCAT
1 TTTTGCA-AATCCGGGGGCATTTTGGTCAT
22281 TTT
1 TTT
22284 GGTTTTATTT
Statistics
Matches: 94, Mismatches: 25, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
29 65 0.69
30 29 0.31
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (29 bp):
TTTTGCAAATCCGGGGGCATTTTGGTCAT
Found at i:22222 original size:58 final size:59
Alignment explanation
Indices: 22134--22283 Score: 214
Period size: 58 Copynumber: 2.6 Consensus size: 59
22124 TTAATTGACA
* * ** *
22134 TTTTGCA-AATCTTGGGGGCATTTTGGTCATTTTTACCCATCCAGGGGTGTTTTGGTCAT
1 TTTTGCACAATC-CGGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCAT
* *
22193 TTTTGCA-TATCCGGGGGTATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCAT
1 TTTTGCACAATCCGGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCAT
22251 TTTTGCACAATCCGGGGGCATTTTGGTCATTTT
1 TTTTGCACAATCCGGGGGCATTTTGGTCATTTT
22284 GGTTTTATTT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 48 0.59
59 33 0.41
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (59 bp):
TTTTGCACAATCCGGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCAT
Done.