Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2316
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: 24086
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1177 original size:67 final size:69
Alignment explanation
Indices: 1068--1213 Score: 242
Period size: 67 Copynumber: 2.1 Consensus size: 69
1058 TTCCAGACTC
*
1068 TTTTTTTATACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGC-AAAA-TTTTTTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGCAAAAATTTTTTTT
1131 TTAT
66 TTAT
*
1135 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAAAAATTTTTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGC--AAAAATTTTTT
1200 TTTTAT
64 TTTTAT
1206 TTTTTTTT
1 TTTTTTTT
1214 ACAAAACCAT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
67 50 0.68
70 4 0.05
71 19 0.26
ACGTcount: A:0.18, C:0.19, G:0.13, T:0.49
Consensus pattern (69 bp):
TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGCAAAAATTTTTTTT
TTAT
Found at i:1959 original size:45 final size:45
Alignment explanation
Indices: 1835--2017 Score: 232
Period size: 45 Copynumber: 4.2 Consensus size: 45
1825 TCGGCCATGG
* * * *
1835 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGG-CCAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
1879 TGCTTCCTTAAATTCTT-CATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
1923 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * *
1968 TGCTTCCTTAATTTGTTCCATAAATTATGC---ATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
2010 TGCTTCCT
1 TGCTTCCT
2018 TAATTTCATG
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
42 19 0.15
43 20 0.16
44 33 0.27
45 52 0.42
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:2346 original size:20 final size:20
Alignment explanation
Indices: 2323--2376 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2313 CAAGTTAAAC
* *
2323 TGAGCTTGAATGAGCTGACT
1 TGAGCTCGAATGAGCTAACT
*
2343 TGAGCACGAATGAGCTAACT
1 TGAGCTCGAATGAGCTAACT
2363 TGAGCTCGAATGAG
1 TGAGCTCGAATGAG
2377 TTGAACCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (20 bp):
TGAGCTCGAATGAGCTAACT
Found at i:2924 original size:18 final size:19
Alignment explanation
Indices: 2896--2935 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
2886 TATTACAAAA
2896 TTAATTAAAATTCATTATG
1 TTAATTAAAATTCATTATG
2915 TTAA-TAAAATTCATTATG
1 TTAATTAAAATTCATTATG
2933 TTA
1 TTA
2936 GTAATTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAATTAAAATTCATTATG
Found at i:8126 original size:20 final size:20
Alignment explanation
Indices: 8087--8126 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
8077 TCTTTCTTTA
8087 ACAGCTTTTAAATCTTCCTTG
1 ACAGCTTTTAAA-CTTCCTTG
8108 ACAGCTTTTACAA-TTCCTT
1 ACAGCTTTTA-AACTTCCTT
8127 TATCTTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (20 bp):
ACAGCTTTTAAACTTCCTTG
Found at i:8712 original size:18 final size:18
Alignment explanation
Indices: 8686--8733 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
8676 TCCCCAGAAC
*
8686 TTTCATGGAAATTGAGAT
1 TTTCGTGGAAATTGAGAT
8704 TTTCGTGGAAAATTGAGAT
1 TTTCGTGG-AAATTGAGAT
*
8723 TTTCGGGGAAA
1 TTTCGTGGAAA
8734 ATGGTTAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.35
Consensus pattern (18 bp):
TTTCGTGGAAATTGAGAT
Found at i:8718 original size:19 final size:19
Alignment explanation
Indices: 8694--8735 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
8684 ACTTTCATGG
*
8694 AAATTGAGATTTTCGTGGA
1 AAATTGAGATTTTCGGGGA
8713 AAATTGAGATTTTCGGGGA
1 AAATTGAGATTTTCGGGGA
8732 AAAT
1 AAAT
8736 GGTTAGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (19 bp):
AAATTGAGATTTTCGGGGA
Found at i:10802 original size:8 final size:9
Alignment explanation
Indices: 10779--10806 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
10769 CCTTTTCCTT
10779 TCTTTTTCA
1 TCTTTTTCA
10788 TCTTTTTCA
1 TCTTTTTCA
10797 TCTTTTTCA
1 TCTTTTTCA
10806 T
1 T
10807 TGCCATTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (9 bp):
TCTTTTTCA
Found at i:12087 original size:19 final size:19
Alignment explanation
Indices: 12020--12092 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
12010 GAAAAATTAT
* *
12020 AAAATTTTATAAATTCATAA
1 AAAATTATA-AAATTCGTAA
*
12040 GAAAATTATAGAAAAAT-GTAA
1 -AAAATTAT--AAAATTCGTAA
*
12061 AGAA-TATAAAATTCGTAA
1 AAAATTATAAAATTCGTAA
12079 AAAATTATAAAATT
1 AAAATTATAAAATT
12093 ATTGTACCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 5 0.12
18 7 0.17
19 12 0.29
20 3 0.07
21 10 0.24
22 4 0.10
23 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (19 bp):
AAAATTATAAAATTCGTAA
Found at i:13302 original size:12 final size:12
Alignment explanation
Indices: 13285--13310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13275 TCAAGAAAAC
13285 AACAACAACAAT
1 AACAACAACAAT
13297 AACAACAACAAT
1 AACAACAACAAT
13309 AA
1 AA
13311 TAGTAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (12 bp):
AACAACAACAAT
Found at i:16423 original size:17 final size:18
Alignment explanation
Indices: 16389--16426 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
16379 GTGTTATTTA
*
16389 AAAACGAGTATCATTTTG
1 AAAACGAGTATCAGTTTG
16407 AAAACGAGTATC-GTTTG
1 AAAACGAGTATCAGTTTG
16424 AAA
1 AAA
16427 CGCGCCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (18 bp):
AAAACGAGTATCAGTTTG
Found at i:21814 original size:36 final size:34
Alignment explanation
Indices: 21767--21859 Score: 105
Period size: 36 Copynumber: 2.7 Consensus size: 34
21757 ATTTTTTTTT
**
21767 TTTTTTTTTTATATATTATTTTTTTACATATTTTA
1 TTTTTTTTTTATATATTATTTTTTTA-ATATTCCA
** *
21802 GTTTTTTTTTTATATGCTATTTTTTTATTATTCCA
1 -TTTTTTTTTTATATATTATTTTTTTAATATTCCA
* *
21837 TTTTTTTTTTTTTTATTATTTTT
1 TTTTTTTTTTATATATTATTTTT
21860 ACTTATATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
34 19 0.40
35 5 0.10
36 24 0.50
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.76
Consensus pattern (34 bp):
TTTTTTTTTTATATATTATTTTTTTAATATTCCA
Found at i:22144 original size:7 final size:7
Alignment explanation
Indices: 22132--22157 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22122 ATATTCTTGT
22132 TATTATA
1 TATTATA
22139 TATTATA
1 TATTATA
22146 TATTATA
1 TATTATA
22153 TATTA
1 TATTA
22158 AATACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTATA
Done.