Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2526
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: 20328
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:315 original size:14 final size:13
Alignment explanation
Indices: 274--344 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
264 GTTTAATTTT
*
274 TAATTTAATCAATA
1 TAATTTAA-AAATA
*
288 TAATTTAATTAATA
1 TAATTTAA-AAATA
302 TATATTTAAAAATA
1 TA-ATTTAAAAATA
*
316 -AATATAAAAATA
1 TAATTTAAAAATA
*
328 TAATTTTTAAAATA
1 TAA-TTTAAAAATA
342 TAA
1 TAA
345 AAAAAATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.20
13 3 0.06
14 30 0.61
15 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATTTAAAAATA
Found at i:496 original size:2 final size:2
Alignment explanation
Indices: 489--516 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
479 AATAATAATA
489 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
517 TTCATTTCTC
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
Found at i:756 original size:19 final size:19
Alignment explanation
Indices: 718--775 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
708 TCATGTGGTC
*
718 AAAAAAATTAAAATACATAAT
1 AAAATAATTAAAAT--ATAAT
739 AAAATAATTAAAATATAAT
1 AAAATAATTAAAATATAAT
*
758 ATAAT-ATTAAAAATATAA
1 AAAATAATT-AAAATATAA
776 ATATATCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.09
19 18 0.53
21 13 0.38
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAATTAAAATATAAT
Found at i:1091 original size:12 final size:12
Alignment explanation
Indices: 1070--1113 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1060 GATAGCTTTG
*
1070 AATATCATATAA
1 AATATAATATAA
1082 AATATAATATAA
1 AATATAATATAA
*
1094 AAAATAATATAA
1 AATATAATATAA
1106 ATATATAA
1 A-ATATAA
1114 ATTTATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAATATAA
Found at i:1695 original size:14 final size:15
Alignment explanation
Indices: 1676--1704 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1666 GGACTGACAT
1676 CTATAATT-TATAAC
1 CTATAATTATATAAC
1690 CTATAATTATATAAC
1 CTATAATTATATAAC
1705 ATCTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (15 bp):
CTATAATTATATAAC
Found at i:1767 original size:2 final size:2
Alignment explanation
Indices: 1760--1788 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1750 TTCAACGCTC
1760 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 A
1789 GTGTCAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2036 original size:11 final size:11
Alignment explanation
Indices: 2022--2047 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2012 TAATAAAATT
2022 ATAAAATAAAA
1 ATAAAATAAAA
2033 ATAAAATAAAA
1 ATAAAATAAAA
2044 ATAA
1 ATAA
2048 TTATGTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:3828 original size:27 final size:27
Alignment explanation
Indices: 3786--3842 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
3776 GGGTACTATG
*
3786 CAACATTCACTGTTTCAAATTGAATTT
1 CAACATTCACTATTTCAAATTGAATTT
*
3813 CAACATTTACTATTTCAAATTGAATTT
1 CAACATTCACTATTTCAAATTGAATTT
3840 CAA
1 CAA
3843 AATTGACGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (27 bp):
CAACATTCACTATTTCAAATTGAATTT
Found at i:3847 original size:13 final size:12
Alignment explanation
Indices: 3798--3848 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
3788 ACATTCACTG
3798 TTTCAAATTGAA
1 TTTCAAATTGAA
*
3810 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
3825 TTTCAAATTGAA
1 TTTCAAATTGAA
3837 TTTCAAAATTGA
1 TTTC-AAATTGA
3849 CGGCACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:17186 original size:2 final size:2
Alignment explanation
Indices: 17179--17207 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17169 CATTAAAACC
17179 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 A
17208 CTTTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.