Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3944
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, 372
Length: 621
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Found at i:124 original size:43 final size:43
Alignment explanation
Indices: 45--464 Score: 483
Period size: 43 Copynumber: 9.8 Consensus size: 43
35 TTTTCGCCAG
* *
45 AAGCGCCGCTAAA-G--TTTGATCTATAGCGGCGTTTGTGGGGA
1 AAGCGCCGCTAAAGGTCTTTG-TCTTTAGCGGCGTTTGTGGGAA
*
86 AAGCGCCGCTAAAGGTCTTTGTTTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
* * * *
129 AAGCGCCGCTAATGGTCTTGGTCTTTAGCGGCGTTT-TCGTGAG
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGT-GGGAA
* * *
172 AAGCGTCGCTAAAGG--TTTGATCTATAGCGGCGTTTGTGGGGA
1 AAGCGCCGCTAAAGGTCTTTG-TCTTTAGCGGCGTTTGTGGGAA
* * * *
214 AAGTGTCACTAAAGGTCTTTGTCTTTAGCGGCGTTTGTAGGAA
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
* * * *
257 AAGCGTCGCTAATGGTCTTTGTCTTTTGCGGCGTTTGTGGGTA
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
* * * *
300 AAGCACCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTTGGAA
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
* * * * *
343 AAGCGCCGCTAATGATCTTGGTCTTTAGCGGCATTTGTGGGAG
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
* *
386 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
* * *
429 AAGCGCCGCTAAAGCTCATGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTT
465 TTTGCAGCGC
Statistics
Matches: 328, Mismatches: 43, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
41 16 0.05
42 31 0.09
43 273 0.83
44 8 0.02
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAA
Found at i:257 original size:128 final size:128
Alignment explanation
Indices: 25--442 Score: 529
Period size: 128 Copynumber: 3.3 Consensus size: 128
15 AGGTTATGTT
**
25 TTTAGCGGCGTTTTCGCCAGAAGCGCCGCTAAA-GTTTGATCTATAGCGGCGTTTGTGGGGAAAG
1 TTTAGCGGCGTTTTCGTGAGAAGCGCCGCTAAAGGTTTGATCTATAGCGGCGTTTGTGGGGAAAG
*
89 CGCCGCTAAAGGTCTTTGTTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTC
66 CGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTC
*
152 TTTAGCGGCGTTTTCGTGAGAAGCGTCGCTAAAGGTTTGATCTATAGCGGCGTTTGTGGGGAAAG
1 TTTAGCGGCGTTTTCGTGAGAAGCGCCGCTAAAGGTTTGATCTATAGCGGCGTTTGTGGGGAAAG
* * * * * *
217 TGTCACTAAAGGTCTTTGTCTTTAGCGGCGTTTGTAGGAAAAGCGTCGCTAATGGTCTTTGTC
66 CGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTC
* * * * * * * *
280 TTTTGCGGCG-TTT-GTGGGTAAAGCACCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTTGGAA
1 TTTAGCGGCGTTTTCGTGAG--AAGCGCCGCTAAAGGT-TTGATCTATAGCGGCGTTTGTGGGGA
* * * * * * *
343 AAGCGCCGCTAATGATCTTGGTCTTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAAGGTCATGGT
63 AAGCGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGT
408 C
128 C
* *
409 TTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTT-TCGTGAGAAGCGCCGCTAAAG
443 CTCATGGTCT
Statistics
Matches: 247, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
126 4 0.02
127 33 0.13
128 109 0.44
129 96 0.39
130 2 0.01
131 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (128 bp):
TTTAGCGGCGTTTTCGTGAGAAGCGCCGCTAAAGGTTTGATCTATAGCGGCGTTTGTGGGGAAAG
CGCCGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTC
Found at i:396 original size:129 final size:129
Alignment explanation
Indices: 45--464 Score: 535
Period size: 129 Copynumber: 3.3 Consensus size: 129
35 TTTTCGCCAG
* *
45 AAGCGCCGCTAAA-GT-TTGATCTATAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTTGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTTGT
* *
108 TTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTCTTTAGCGGCGTTT-T-CGTGA
66 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTGGGT-A
* * * * * *
171 GAAGCGTCGCTAAAGGT-TTGATCTATAGCGGCGTTTGTGGGGAAAGTGTCACTAAAGGTCTTTG
1 -AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTTG
* * * *
235 TCTTTAGCGGCGTTTGTAGGAAAAGCGTCGCTAATGGTCTTTGTCTTTTGCGGCGTTTGTGGGTA
65 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTGGGTA
* * * * * * *
300 AAGCACCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAATGATCTTGGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTTGT
* * * * *
365 CTTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
66 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTGGGTA
* *
429 AAGCGCCGCTAAAGCTCATGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
465 TTTGCAGCGC
Statistics
Matches: 253, Mismatches: 36, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
127 12 0.05
128 112 0.44
129 127 0.50
130 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (129 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTTGT
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAATGGTCTTGGTCTTTAGCGGCGTTTGTGGGTA
Done.