Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold377
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: 400731
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.31
Warning! 22032 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:379876 original size:3 final size:3
Alignment explanation
Indices: 379868--379895 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
379858 GCTCTATCGA
379868 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
379896 AGAATCCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:386121 original size:16 final size:18
Alignment explanation
Indices: 386100--386135 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
386090 TTTTATGTGT
386100 TATAAAT-TAA-ATAATA
1 TATAAATATAACATAATA
386116 TATAAATATAACATAATA
1 TATAAATATAACATAATA
386134 TA
1 TA
386136 AAACATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:388868 original size:15 final size:15
Alignment explanation
Indices: 388851--388883 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
388841 AAGGTATAAT
388851 AAAATATTAAAAAATA
1 AAAAT-TTAAAAAATA
388867 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
388882 AA
1 AA
388884 GACATATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:392527 original size:29 final size:29
Alignment explanation
Indices: 392495--392550 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
392485 AAAAGCCGTT
392495 TTTTTTCAA-AATTTACCGGAATGGGCCGG
1 TTTTTT-AATAATTTACCGGAATGGGCCGG
*
392524 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGGAATGGGCC
392551 ATTTTTCACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGGAATGGGCCGG
Found at i:393158 original size:19 final size:20
Alignment explanation
Indices: 393125--393172 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
393115 GTGGTGCTCG
393125 AAGTGCATCACTGGCACACA
1 AAGTGCATCACTGGCACACA
*
393145 AAGTGCAT-ACTGGCACATA
1 AAGTGCATCACTGGCACACA
*
393164 AGGTGCATC
1 AAGTGCATC
393173 TTGGTGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (20 bp):
AAGTGCATCACTGGCACACA
Found at i:394531 original size:27 final size:27
Alignment explanation
Indices: 394490--394592 Score: 154
Period size: 27 Copynumber: 3.8 Consensus size: 27
394480 TAGTATTGGC
*
394490 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
394517 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
394544 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
**
394571 GCC-ATACTGAAAGGCGCCAATG
1 GCCTAT-CTGGGAGGCGCCAATG
394593 CTGTGATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 2 0.03
27 68 0.97
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.21
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:395575 original size:3 final size:3
Alignment explanation
Indices: 395569--395604 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
395559 TTTTTTTTCT
*
395569 TTC TTC TTC TTC TTC TTC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
395605 CCTTTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:398895 original size:3 final size:3
Alignment explanation
Indices: 398887--398928 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
398877 GATTTAGTCC
* *
398887 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
398929 GTTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:399302 original size:16 final size:16
Alignment explanation
Indices: 399277--399313 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
399267 TATACCCACG
* *
399277 TATATGTACATATTTT
1 TATATATACATATTTA
399293 TATATATACATATTTA
1 TATATATACATATTTA
399309 TATAT
1 TATAT
399314 TCTTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (16 bp):
TATATATACATATTTA
Found at i:399332 original size:21 final size:21
Alignment explanation
Indices: 399308--399351 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
399298 ATACATATTT
* * *
399308 ATATATTCTTTATATTTTTTA
1 ATATATTATATATATTTTATA
399329 ATATATTATATATATTTTATA
1 ATATATTATATATATTTTATA
399350 AT
1 AT
399352 TCACATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTATATATATTTTATA
Found at i:400665 original size:19 final size:19
Alignment explanation
Indices: 400641--400677 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
400631 ATCATCGATT
400641 TAGTTTTTAAAACTTTAGC
1 TAGTTTTTAAAACTTTAGC
400660 TAGTTTTTAAAACTTTAG
1 TAGTTTTTAAAACTTTAG
400678 ATTTCGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (19 bp):
TAGTTTTTAAAACTTTAGC
Done.