Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_429 ID=scaffold_429-JGI_221_v2.0
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: 7138
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Found at i:1413 original size:40 final size:40
Alignment explanation
Indices: 1369--1449 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1359 GTAGCTTACA
1369 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
1 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
1409 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
1 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
1449 T
1 T
1450 GTGTCATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (40 bp):
TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
Found at i:2037 original size:9 final size:9
Alignment explanation
Indices: 2023--2047 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2013 GTGATTCTCG
2023 AAGTTCATC
1 AAGTTCATC
2032 AAGTTCATC
1 AAGTTCATC
2041 AAGTTCA
1 AAGTTCA
2048 ATCTTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (9 bp):
AAGTTCATC
Found at i:4569 original size:49 final size:49
Alignment explanation
Indices: 4516--4663 Score: 278
Period size: 49 Copynumber: 3.0 Consensus size: 49
4506 ACAACTCTTG
4516 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
1 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
*
4565 TTCTAAACATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
1 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
*
4614 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCCAGGTTTCTAA
1 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
4663 T
1 T
4664 CCTATTAGAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 96 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (49 bp):
TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
Found at i:5940 original size:27 final size:27
Alignment explanation
Indices: 5853--5940 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
5843 AAGGTTGTTC
*
5853 AAATAACCAAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
5880 AAATGAACAAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
5907 AAATGACCGAAATACCTCCATAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
5934 AAATGAC
1 AAATGAC
5941 TGTTATACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Done.