Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1848
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: 17554
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Found at i:1056 original size:16 final size:17
Alignment explanation
Indices: 1035--1067 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1025 ATTTAAGGTA
1035 AAGTTT-CAATTAAAAT
1 AAGTTTACAATTAAAAT
1051 AAGTTTACAATTAAAAT
1 AAGTTTACAATTAAAAT
1068 TTTAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
AAGTTTACAATTAAAAT
Found at i:1374 original size:78 final size:78
Alignment explanation
Indices: 1245--1400 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
1235 AATGCTTTGA
* *
1245 AAATCTTCTAGACAACTTGCATTGAGGACTACAAAGGTTATCAATATGAATGGATCACAATTCTT
1 AAATCTTCTAGACAACCTGCATTGAGGACTACAAAGGTTATCAATATGAATGGATCACAATTCCT
1310 ATATGGGACTAGC
66 ATATGGGACTAGC
* *
1323 AAATCTTCTAGACAACCTGCATTGAGGATTATAAAGGTTATCAATATGAATGGATCACAATTCCT
1 AAATCTTCTAGACAACCTGCATTGAGGACTACAAAGGTTATCAATATGAATGGATCACAATTCCT
1388 ATATGGGACTAGC
66 ATATGGGACTAGC
1401 TTGTTAAGCT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (78 bp):
AAATCTTCTAGACAACCTGCATTGAGGACTACAAAGGTTATCAATATGAATGGATCACAATTCCT
ATATGGGACTAGC
Found at i:3115 original size:18 final size:18
Alignment explanation
Indices: 3066--3107 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3056 AAATTAAGGG
* *
3066 TAAAATTATAAAATA-AT
1 TAAAAATATAATATACAT
*
3083 TAAAAATATATTATACAT
1 TAAAAATATAATATACAT
3101 TAAAAAT
1 TAAAAAT
3108 TCAATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAATATAATATACAT
Found at i:6685 original size:15 final size:15
Alignment explanation
Indices: 6655--6684 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6645 ACTAATAATG
6655 ATTAATATATTAAAA
1 ATTAATATATTAAAA
6670 ATTAATA-ATTAAAA
1 ATTAATATATTAAAA
6684 A
1 A
6685 AATAATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAATATATTAAAA
Found at i:7909 original size:27 final size:28
Alignment explanation
Indices: 7879--7943 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
7869 TATCGGTTAA
*
7879 TAATATTGATTTTGGTAAG-AATTTATT
1 TAATATTGATTTTGGTAAGAAACTTATT
7906 TAATATTGATTTTGGTAAGAAACTTATT
1 TAATATTGATTTTGGTAAGAAACTTATT
*
7934 TATTA-TGATT
1 TAATATTGATT
7944 AAAACTTGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.51
Consensus pattern (28 bp):
TAATATTGATTTTGGTAAGAAACTTATT
Found at i:8772 original size:18 final size:18
Alignment explanation
Indices: 8746--8780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8736 GAATATCAAG
8746 TTTTAAAAAATAAATTTA
1 TTTTAAAAAATAAATTTA
* *
8764 TTTTTAAAAATTAATTT
1 TTTTAAAAAATAAATTT
8781 TAAGAAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAAAATAAATTTA
Found at i:12782 original size:75 final size:75
Alignment explanation
Indices: 12565--12813 Score: 333
Period size: 75 Copynumber: 3.3 Consensus size: 75
12555 GGCAAGATGA
* * ** *
12565 AACAA-TAATCCGAGATAATCTGCATGATAATTACAATCAACAAATGTTTCAACATATTTCATAG
1 AACAACTAATCCGAGATAATCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCATAT
12629 TACTACTATC
66 TACTACTATC
* * * * *
12639 AACAACTAATCTGAGATAATCTGGCACGATAACTACAAGCAACAATAT-TTTTTGCATTTTTCAC
1 AACAACTAATCCGAGATAATCT-GCACGATAACTACAATCAACAA-ATGTTTCTGCATATTTCAT
12703 ATTACTACTATC
64 ATTACTACTATC
*
12715 AACAACTAATCCGAGATAATCTGTACGATAACTACAATCAACAAATGTTTCTGCATATTTCATAT
1 AACAACTAATCCGAGATAATCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCATAT
*
12780 TACTACTATT
66 TACTACTATC
* *
12790 AATAACGAAT-CGAGATAATCTGCA
1 AACAACTAATCCGAGATAATCTGCA
12814 TATTTCATAT
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
74 20 0.13
75 67 0.44
76 62 0.41
77 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (75 bp):
AACAACTAATCCGAGATAATCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCATAT
TACTACTATC
Found at i:13150 original size:27 final size:27
Alignment explanation
Indices: 13099--13155 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
13089 GGGTCATGGC
** * *
13099 AGGATATGTTGGGTATGAAGGTTGAGT
1 AGGATATGACGGGTATGAAGATTGAAT
*
13126 AGGATATGACGGGTATGGAGATTGAAT
1 AGGATATGACGGGTATGAAGATTGAAT
13153 AGG
1 AGG
13156 GAAATATGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.40, T:0.28
Consensus pattern (27 bp):
AGGATATGACGGGTATGAAGATTGAAT
Done.