Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2722
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: 64112
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1161 original size:20 final size:20
Alignment explanation
Indices: 1128--1165 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1118 TTTTGGGTTT
1128 AATTTAAATATAATATTTTTA
1 AATTTAAATATAAT-TTTTTA
*
1149 AATTT-AATTTAATTTTT
1 AATTTAAATATAATTTTT
1166 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 7 0.44
21 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTAAATATAATTTTTTA
Found at i:1173 original size:19 final size:18
Alignment explanation
Indices: 1142--1177 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1132 TAAATATAAT
1142 ATTTTTAAATTTAATTTA
1 ATTTTTAAATTTAATTTA
*
1160 ATTTTTAATTTTTAATTT
1 ATTTTTAA-ATTTAATTT
1178 TTTAAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAAATTTAATTTA
Found at i:2793 original size:16 final size:16
Alignment explanation
Indices: 2768--2801 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2758 ATGTTTAAAT
*
2768 AATAATAATTAATTTA
1 AATAAAAATTAATTTA
*
2784 AATAAAAATTATTTTA
1 AATAAAAATTAATTTA
2800 AA
1 AA
2802 GATAATCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAAAATTAATTTA
Found at i:2880 original size:16 final size:16
Alignment explanation
Indices: 2861--2892 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2851 CATTAAAATA
2861 TAATTTAATCATAATT
1 TAATTTAATCATAATT
2877 TAATTTAATCATAATT
1 TAATTTAATCATAATT
2893 AACAGATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTAATCATAATT
Found at i:4983 original size:2 final size:2
Alignment explanation
Indices: 4976--5010 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4966 CCCCTTGTTG
4976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5011 AAGTTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6958 original size:2 final size:2
Alignment explanation
Indices: 6951--6977 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6941 GGAAAACCAC
6951 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6978 ACTTAGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10735 original size:13 final size:12
Alignment explanation
Indices: 10705--10734 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10695 TTTAAGTTGT
*
10705 ATTTTTAGTTAA
1 ATTTTTAATTAA
10717 ATTTTTAATTAA
1 ATTTTTAATTAA
10729 ATTTTT
1 ATTTTT
10735 TTGTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
ATTTTTAATTAA
Found at i:11897 original size:2 final size:2
Alignment explanation
Indices: 11885--11919 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11875 GAAGACAAAT
*
11885 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11920 TGGTGTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13358 original size:2 final size:2
Alignment explanation
Indices: 13353--13378 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13343 GTATTTTCTT
13353 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
13379 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13383 original size:2 final size:2
Alignment explanation
Indices: 13378--13421 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
13368 ATATATATAT
13378 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13420 AG
1 AG
13422 TTCAACGTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37249 original size:2 final size:2
Alignment explanation
Indices: 37242--37281 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
37232 GCTTGGACAG
*
37242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37282 AAATTAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44037 original size:2 final size:2
Alignment explanation
Indices: 44032--44072 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
44022 AGGGGGGGGG
*
44032 GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
44073 GAAATGAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45978 original size:14 final size:14
Alignment explanation
Indices: 45956--45997 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
45946 ATAAATTTTT
45956 TTATAATAAATAAA
1 TTATAATAAATAAA
*
45970 TTATTATAAATAAA
1 TTATAATAAATAAA
45984 -TATAA-AACATAAA
1 TTATAATAA-ATAAA
45997 T
1 T
45998 AAAATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 2 0.08
13 9 0.38
14 13 0.54
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TTATAATAAATAAA
Found at i:45983 original size:18 final size:19
Alignment explanation
Indices: 45945--45985 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
45935 AATACTCTTG
* *
45945 AATAAATTTTTTTATAATA
1 AATAAATTATTATATAATA
45964 AATAAATTATTATA-AATA
1 AATAAATTATTATATAATA
45982 AATA
1 AATA
45986 TAAAACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATAAATTATTATATAATA
Found at i:47715 original size:27 final size:26
Alignment explanation
Indices: 47659--47715 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
47649 ATGTCAAATT
* * *
47659 TTTATTTAATTAAAAATATTTTATTA
1 TTTATTTAATTAAAAAAAATTTAATA
* *
47685 TTTATTTTATGTAAAAAAAATTTAATC
1 TTTATTTAAT-TAAAAAAAATTTAATA
47712 TTTA
1 TTTA
47716 AGAATATTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTATTTAATTAAAAAAAATTTAATA
Found at i:49009 original size:15 final size:16
Alignment explanation
Indices: 48979--49012 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
48969 CTTCTGACCA
48979 TTTCTTTCTCTCTTTT
1 TTTCTTTCTCTCTTTT
*
48995 TTTCTTT-TTTCTTTT
1 TTTCTTTCTCTCTTTT
49010 TTT
1 TTT
49013 AAGCATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTCTCTCTTTT
Found at i:59593 original size:1 final size:1
Alignment explanation
Indices: 59583--59675 Score: 78
Period size: 1 Copynumber: 93.0 Consensus size: 1
59573 TGGCAATTGG
* * * ** * * * **
59583 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
59648 AAAGAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
59676 GTGAAGATTT
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:59632 original size:34 final size:34
Alignment explanation
Indices: 59584--59676 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 34
59574 GGCAATTGGA
59584 AAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAAGGAAAAAG
59619 AAAAAAAAAAACAAAAC-AAAAAAAAGGAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAAGGAAAAAG
*
59652 AAAAAAAAAAA-AACA-AAAAAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAAG
59677 TGAAGATTTG
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
32 12 0.21
33 27 0.48
34 13 0.23
35 4 0.07
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAACAAAACAAAAAAAAAGGAAAAAG
Found at i:63428 original size:2 final size:2
Alignment explanation
Indices: 63421--63448 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
63411 AAGCCTGCTA
63421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63449 GTAGTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.