Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1021
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: 3295
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.28
Warning! 595 characters in sequence are not A, C, G, or T
Found at i:74 original size:25 final size:25
Alignment explanation
Indices: 45--110 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
35 ATCATTATAT
45 GTAAGATTTTACGAATAATGATGTA
1 GTAAGATTTTACGAATAATGATGTA
70 GTAAGATTTTACGAATAATGATGTA
1 GTAAGATTTTACGAATAATGATGTA
95 GTAAGATTTTACGAAT
1 GTAAGATTTTACGAAT
111 GTTTAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (25 bp):
GTAAGATTTTACGAATAATGATGTA
Found at i:1784 original size:21 final size:21
Alignment explanation
Indices: 1758--1798 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1748 AACTTAAAAC
* *
1758 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCCGCAGCGAGAGAAGT
1779 AGAGGCCGCAGCGAGAGAAG
1 AGAGGCCGCAGCGAGAGAAG
1799 CAGTGAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.49, T:0.02
Consensus pattern (21 bp):
AGAGGCCGCAGCGAGAGAAGT
Found at i:2284 original size:43 final size:43
Alignment explanation
Indices: 2237--2351 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
2227 ATCATATAGT
*
2237 GGCGTTTCTGAAAT-AAGCGCCGCTAAAGCACACTACTTTTAGC
1 GGCGTTTCT-AAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
* * **
2280 GGCGTTTGTAGATAAAGCGCCGCTAAAGAACTTTACTTTTAGC
1 GGCGTTTCTAAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
*
2323 GGCGTTT-T-ATTCACAAGCGCCGCTAAAGA
1 GGCGTTTCTAAAT-A-AAGCGCCGCTAAAGA
2352 TGATGGTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 5 0.08
43 56 0.90
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (43 bp):
GGCGTTTCTAAATAAAGCGCCGCTAAAGAACACTACTTTTAGC
Found at i:2434 original size:42 final size:42
Alignment explanation
Indices: 2250--2599 Score: 366
Period size: 43 Copynumber: 8.2 Consensus size: 42
2240 GTTTCTGAAA
* * ***
2250 TAAGCGCCGCTAAAGCACACT-A-CTTTTAGCGGCGTTTGTAGA
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTTC
* * *
2292 TAAAGCGCCGCTAAAGAACTTTA-CTTTTAGCGGCGTTTTATTC
1 T-AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTTC
* ** * *
2335 ACAAGCGCCGCTAAAGATGATGGTCTTTAGCGGCGTTTTTTGC
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * * * *
2378 ACAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTTTC
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
2421 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
2463 TAAGCACCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-C
* *
2506 TAAGCGCCGCTAAAGAACACGATCTTTAGTGGC-TTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
2547 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TC
2590 TAAGCGCCGC
1 TAAGCGCCGC
2600 AAAAAGTTAG
Statistics
Matches: 263, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
41 31 0.12
42 88 0.33
43 143 0.54
44 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:2499 original size:84 final size:83
Alignment explanation
Indices: 2294--2599 Score: 362
Period size: 84 Copynumber: 3.6 Consensus size: 83
2284 TTTGTAGATA
* * * * * ** *
2294 AAGCGCCGCTAAAGAACTTTA-CTTTTAGCGGCGTTTTATTCACAAGCGCCGCTAAAGATGATGG
1 AAGCGCCGCTAAAGATCATGATC-TTTAGCGGCGTTTTTTTC-TAAGCGCCGCTAAAGAACATGA
* *
2358 TCTTTAGCGGCGTTTTTTGCAC
64 TCTTTAGCGGC-TTTTTTTC-T
* * *
2380 AAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
2445 TTTAGCGGCTTTTTTTTCT
66 TTTAGCGGC-TTTTTTTCT
* * *
2464 AAGCACCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACACGAT
1 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTT-CTAAGCGCCGCTAAAGAACATGAT
*
2529 CTTTAGTGGCTTTTTTTCT
65 CTTTAGCGGCTTTTTTTCT
* * *
2548 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCTGTAAGCGCCGC
1 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTT-TCTAAGCGCCGC
2600 AAAAAGTTAG
Statistics
Matches: 192, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
84 90 0.47
85 69 0.36
86 32 0.17
87 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (83 bp):
AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCTTTTTTTCT
Found at i:2993 original size:19 final size:20
Alignment explanation
Indices: 2969--3006 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2959 AAATTACAAT
2969 ATTTTTATAACTTT-TTTTC
1 ATTTTTATAACTTTATTTTC
*
2988 ATTTTTATATCTTTATTTT
1 ATTTTTATAACTTTATTTT
3007 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATAACTTTATTTTC
Done.