Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1891
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: 50583
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:3319 original size:38 final size:39
Alignment explanation
Indices: 3235--3369 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
3225 ACCAATATGG
*
3235 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
3274 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
3312 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
3353 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3370 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:4943 original size:5 final size:5
Alignment explanation
Indices: 4925--4955 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
4915 TTTCTTTTAT
4925 ATATA ATAATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA
4956 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:9075 original size:21 final size:20
Alignment explanation
Indices: 9049--9092 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
9039 CATTTAATTA
*
9049 ATTTTTTAAAATTTTAAAAAC
1 ATTTTTTAAAA-TTAAAAAAC
9070 ATTTTTTAAAATTAAAAAAC
1 ATTTTTTAAAATTAAAAAAC
9090 ATT
1 ATT
9093 AAAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTTTAAAATTAAAAAAC
Found at i:9461 original size:26 final size:26
Alignment explanation
Indices: 9425--9476 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
9415 CTACCCTATG
9425 GAGATAGTTTGCAATTAGACAAAGCA
1 GAGATAGTTTGCAATTAGACAAAGCA
9451 GAGATAGTTTGCAATTAGACAAAGCA
1 GAGATAGTTTGCAATTAGACAAAGCA
9477 TTAGTTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (26 bp):
GAGATAGTTTGCAATTAGACAAAGCA
Found at i:18029 original size:17 final size:16
Alignment explanation
Indices: 17997--18027 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17987 TACTTAAAGT
17997 TTTAGTTATATTTTTG
1 TTTAGTTATATTTTTG
18013 TTTAGTTATATTTTT
1 TTTAGTTATATTTTT
18028 TGGTGCCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (16 bp):
TTTAGTTATATTTTTG
Found at i:22481 original size:21 final size:22
Alignment explanation
Indices: 22442--22488 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
22432 TAGTAAGAAT
*
22442 AAAAATGTTTTCTAAAATT-TA
1 AAAAATGTTTGCTAAAATTGTA
* *
22463 AAAAATGTTTGGTATAATTGTA
1 AAAAATGTTTGCTAAAATTGTA
22485 AAAA
1 AAAA
22489 TAATAATGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAAATGTTTGCTAAAATTGTA
Found at i:25688 original size:21 final size:23
Alignment explanation
Indices: 25637--25688 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
25627 GGGGGCCAAA
25637 ATTAAATTATAACTTTTATAATAG
1 ATTAAA-TATAACTTTTATAATAG
*
25661 -TAAAAATATAA-TTTT-TAATAG
1 AT-TAAATATAACTTTTATAATAG
25682 ATTAAAT
1 ATTAAAT
25689 CAAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 6 0.25
24 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTAAATATAACTTTTATAATAG
Found at i:48805 original size:14 final size:14
Alignment explanation
Indices: 48775--48803 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
48765 TTTTTTAATA
48775 TTATATTAATTTTT
1 TTATATTAATTTTT
48789 TTATA-TAATTTTT
1 TTATATTAATTTTT
48802 TT
1 TT
48804 TAATATTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATATTAATTTTT
Found at i:49236 original size:23 final size:22
Alignment explanation
Indices: 49210--49253 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
49200 CACTCGAAAT
49210 CATTATA-AACTTAATTTTATATC
1 CATTATATAA-TT-ATTTTATATC
*
49233 CATTTTATAATTATTTTATAT
1 CATTATATAATTATTTTATAT
49254 ATTAGAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
CATTATATAATTATTTTATATC
Done.