Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_648 ID=scaffold_648-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: 4962
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Found at i:103 original size:16 final size:16
Alignment explanation
Indices: 60--107 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
50 TAGGAGGTTG
* * *
60 CTACTAAACTAATGAA
1 CTACTGAACTATTGAT
76 CTACTGAACTATTGAT
1 CTACTGAACTATTGAT
*
92 CTACTGAGCTATTGAT
1 CTACTGAACTATTGAT
108 TTAAGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (16 bp):
CTACTGAACTATTGAT
Found at i:423 original size:22 final size:22
Alignment explanation
Indices: 395--437 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
385 GTGTGGCTAC
395 TATTA-TTATTGTTATATTCATT
1 TATTATTTATT-TTATATTCATT
*
417 TATTATTTATTTTATCTTCAT
1 TATTATTTATTTTATATTCAT
438 GTTTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATTTATTTTATATTCATT
Found at i:1535 original size:136 final size:135
Alignment explanation
Indices: 1291--1558 Score: 511
Period size: 136 Copynumber: 2.0 Consensus size: 135
1281 CTTAGTGAGC
1291 ATGATTCGTGCTTTAAAATTGTTGATGTAAATTAACCGAGTTTGCACGTTCGAGTCGTAAAAGTA
1 ATGATTCGTGCTTTAAAATTGTTGATGTAAATTAACCGAGTTTGCACGTTCGAGTCGTAAAAGTA
1356 AGACAATAGAGAAAAGAAATGAGAGAAAGCTCACTCGTCATCTATGCATGACTTAGTTTTTGTTC
66 AGACAATAGAGAAAAGAAATGAGAGAAAGCTCACTCGTCATCTATGCATGACTTAG-TTTTGTTC
1421 TGTGCT
130 TGTGCT
1427 ATGATTCGTGCTTTAAAATTGTTGATGTAAATTAACCGAGTTTGCACGTTCGAGTCGTAAAAGTA
1 ATGATTCGTGCTTTAAAATTGTTGATGTAAATTAACCGAGTTTGCACGTTCGAGTCGTAAAAGTA
1492 AGACAATAGAGAAAAGAAATGAGAGAAAAGCTCACT-GTCATCTATGCATGACTTAGTTTTGTTC
66 AGACAATAGAGAAAAGAAATGAGAG-AAAGCTCACTCGTCATCTATGCATGACTTAGTTTTGTTC
1556 TGT
130 TGT
1559 ATAACATCTA
Statistics
Matches: 131, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
135 11 0.08
136 110 0.84
137 10 0.08
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (135 bp):
ATGATTCGTGCTTTAAAATTGTTGATGTAAATTAACCGAGTTTGCACGTTCGAGTCGTAAAAGTA
AGACAATAGAGAAAAGAAATGAGAGAAAGCTCACTCGTCATCTATGCATGACTTAGTTTTGTTCT
GTGCT
Found at i:2942 original size:17 final size:18
Alignment explanation
Indices: 2920--2960 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
2910 TAATTGAATG
2920 AATTGAATAGAT-ATTGA
1 AATTGAATAGATGATTGA
*
2937 AATTGAATATATGATTGA
1 AATTGAATAGATGATTGA
2955 AATTGA
1 AATTGA
2961 TCGAATTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (18 bp):
AATTGAATAGATGATTGA
Done.