Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1843
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: 22782
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:12342 original size:30 final size:30
Alignment explanation
Indices: 12306--12471 Score: 206
Period size: 30 Copynumber: 5.5 Consensus size: 30
12296 TTTGGTTATT
* *
12306 AATTATGAAAAGAGATAGTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
*
12336 AATTATGAAAAGGGATAGTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
*** * *
12366 AATTATGAAAAGGGATGGTTTTGGCTATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
* *
12396 CATTATGAAAAGGGATGGTGACGACCATCG
1 AATTATGAAAAGGGATGGTGACGACCATCA
** *
12426 AACAATGAAAAGGGATGGTGGCGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
*
12456 AATTATGAAATGGGAT
1 AATTATGAAAAGGGAT
12472 AGCTTCGACT
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 114 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (30 bp):
AATTATGAAAAGGGATGGTGACGACCATCA
Found at i:12434 original size:90 final size:89
Alignment explanation
Indices: 12281--12471 Score: 265
Period size: 90 Copynumber: 2.1 Consensus size: 89
12271 TCATCGATGA
* * **
12281 ATGAAAAGGGATGACTTTGGTTATTAATTATGAAAAGAGATAGTGACGACCATCAAATTATGAAA
1 ATGAAAAGGGATGACTTTGGCTATCAATTATGAAAAGAGATAGTGACGACCATCAAACAATGAAA
12346 AGGGATAGTGACGACCATCAAATT
66 AGGGATAGTGACGACCATCAAATT
** * * *
12370 ATGAAAAGGGATGGTTTTGGCTATCACATTATGAAAAGGGATGGTGACGACCATCGAACAATGAA
1 ATGAAAAGGGATGACTTTGGCTATCA-ATTATGAAAAGAGATAGTGACGACCATCAAACAATGAA
* *
12435 AAGGGATGGTGGCGACCATCAAATT
65 AAGGGATAGTGACGACCATCAAATT
*
12460 ATGAAATGGGAT
1 ATGAAAAGGGAT
12472 AGCTTCGACT
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 22 0.25
90 67 0.75
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (89 bp):
ATGAAAAGGGATGACTTTGGCTATCAATTATGAAAAGAGATAGTGACGACCATCAAACAATGAAA
AGGGATAGTGACGACCATCAAATT
Found at i:12484 original size:90 final size:91
Alignment explanation
Indices: 12307--12501 Score: 252
Period size: 90 Copynumber: 2.2 Consensus size: 91
12297 TTGGTTATTA
* **
12307 ATTATGAAAAGAGATAGTGACGACCATCAAATTATGAAAAGGGATAGTGACGACCATCAAATTAT
1 ATTATGAAAAGGGATAGTGACGACCATCAAACAATGAAAAGGGATAGTGACGACCATCAAATTAT
* * * *
12372 GAAAAGGGATGGTTTTGGCTATC-AC
66 GAAAAGGGATAGCTTCGACTATCGAC
* * * *
12397 ATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGTGGCGACCATCAAATTAT
1 ATTATGAAAAGGGATAGTGACGACCATCAAACAATGAAAAGGGATAGTGACGACCATCAAATTAT
* *
12462 GAAATGGGATAGCTTCGACTATCGAG
66 GAAAAGGGATAGCTTCGACTATCGAC
12488 A-TATG-AAAGGGATA
1 ATTATGAAAAGGGATA
12502 ATTTCGGTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
89 8 0.09
90 80 0.89
91 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (91 bp):
ATTATGAAAAGGGATAGTGACGACCATCAAACAATGAAAAGGGATAGTGACGACCATCAAATTAT
GAAAAGGGATAGCTTCGACTATCGAC
Found at i:16404 original size:15 final size:17
Alignment explanation
Indices: 16386--16417 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16376 TAGCATAATT
16386 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
16401 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
16418 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:20011 original size:23 final size:23
Alignment explanation
Indices: 19985--20048 Score: 56
Period size: 28 Copynumber: 2.6 Consensus size: 23
19975 GATGGATTAT
19985 ATTATTCTGGTGTATTTGGGAGG
1 ATTATTCTGGTGTATTTGGGAGG
* *
20008 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTATTTGGGAGG
*
20036 ATTATACTGGTGT
1 ATTATTCTGGTGT
20049 GTTTTGGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
23 8 0.24
24 1 0.03
25 3 0.09
26 3 0.09
27 2 0.06
28 16 0.48
ACGTcount: A:0.20, C:0.05, G:0.31, T:0.44
Consensus pattern (23 bp):
ATTATTCTGGTGTATTTGGGAGG
Found at i:20011 original size:28 final size:28
Alignment explanation
Indices: 19958--20041 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
19948 CACTTTGTGC
19958 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
19987 TATTCTGGTGTATTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
20015 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
20042 CTGGTGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Done.