Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1321
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: 26212
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1722 original size:27 final size:27
Alignment explanation
Indices: 1691--1743 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1681 TTGTGCGAGA
*
1691 TACTAATTCCGGGCTAAATCCGAAGGT
1 TACTAAATCCGGGCTAAATCCGAAGGT
* *
1718 TACTAAATCCGGGTTAAGTCCGAAGG
1 TACTAAATCCGGGCTAAATCCGAAGG
1744 CATTTGTGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (27 bp):
TACTAAATCCGGGCTAAATCCGAAGGT
Found at i:9634 original size:31 final size:28
Alignment explanation
Indices: 9592--9683 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 28
9582 CCATATCCGG
9592 ACTAAGATCCGAAGGCATTTGTGCGAGAT
1 ACTAAG-TCCGAAGGCATTTGTGCGAGAT
9621 ACTAATTGCTCCGAAGGCA--T-TGCGAGA-
1 ACTAA--G-TCCGAAGGCATTTGTGCGAGAT
*
9648 A-TAAGTCCGAAGGCATTTGT-CGAGTT
1 ACTAAGTCCGAAGGCATTTGTGCGAGAT
*
9674 ACTAAATCCG
1 ACTAAGTCCG
9684 GGTTAAGTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
23 10 0.19
24 1 0.02
25 5 0.09
26 5 0.09
27 8 0.15
28 7 0.13
29 6 0.11
31 11 0.21
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (28 bp):
ACTAAGTCCGAAGGCATTTGTGCGAGAT
Found at i:9721 original size:40 final size:40
Alignment explanation
Indices: 9649--9785 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
9639 ATTGCGAGAA
9649 TAAGT-CCGAAGGCATTTGT-CGAGTTACTAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
9687 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
*
9727 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGT
*
9767 TATGTCCCGAAGGCATTTG
1 TAAGTCCCGAAGGCATTTG
9786 AACGAGGAGC
Statistics
Matches: 94, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
38 5 0.05
39 14 0.15
40 73 0.78
41 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
Found at i:9803 original size:80 final size:77
Alignment explanation
Indices: 9649--9818 Score: 209
Period size: 80 Copynumber: 2.2 Consensus size: 77
9639 ATTGCGAGAA
* ** *
9649 TAAGTCCGAAGGCATTTGTCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTT
1 TAAGTCCGAAGGCATTTGTCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTG
9714 ACTAAATCCGGGT
66 ACTAAATCC-GGT
*
9727 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGT-CCGAAGGCATTTGT-CGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGA
*
9791 G-GAGCTATATCCGGT
63 GTGA-CTAAATCCGGT
*
9806 TAAATTCCGAAGG
1 T-AAGTCCGAAGG
9819 TACGTGATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
78 5 0.06
79 26 0.32
80 47 0.59
81 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (77 bp):
TAAGTCCGAAGGCATTTGTCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTG
ACTAAATCCGGT
Found at i:12105 original size:22 final size:22
Alignment explanation
Indices: 12058--12130 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
12048 GATAACAGTG
*
12058 AGCTCGATTGAGCTGAAACCGGGA
1 AGCTCTATTGAGCT-AAA-CGGGA
12082 AGCTCTATTGAGCTAAACGGGA
1 AGCTCTATTGAGCTAAACGGGA
* *
12104 AGCTCT-TTCGAGCTGAACAGGA
1 AGCTCTATT-GAGCTAAACGGGA
12126 AGCTC
1 AGCTC
12131 ATACGAGCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
21 2 0.04
22 27 0.60
23 3 0.07
24 13 0.29
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.21
Consensus pattern (22 bp):
AGCTCTATTGAGCTAAACGGGA
Found at i:12137 original size:22 final size:22
Alignment explanation
Indices: 12091--12140 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
12081 AAGCTCTATT
* * *
12091 GAGCTAAACGGGAAGCTCTTTC
1 GAGCTAAACAGGAAGCTCATAC
*
12113 GAGCTGAACAGGAAGCTCATAC
1 GAGCTAAACAGGAAGCTCATAC
12135 GAGCTA
1 GAGCTA
12141 TGGTGAGTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (22 bp):
GAGCTAAACAGGAAGCTCATAC
Found at i:13521 original size:44 final size:42
Alignment explanation
Indices: 13421--13531 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 42
13411 CGATGCCACT
* * * *
13421 GTCCCAGATAGGGTCTTACACGAAATTAGATACGATGTCGAT
1 GTCCCAGATATGGTCTTACACGAAAATAGAAACGATGTCGAC
* *
13463 GTCCTAGACATGGTCTTACACGTAAAATAGAAATCGATG-CGAAC
1 GTCCCAGATATGGTCTTACACG-AAAATAGAAA-CGATGTCG-AC
* *
13507 GTCCCAAATATGGTCTTACATGAAA
1 GTCCCAGATATGGTCTTACACGAAA
13532 TCCTATGTCA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 19 0.34
43 13 0.23
44 24 0.43
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
GTCCCAGATATGGTCTTACACGAAAATAGAAACGATGTCGAC
Found at i:17328 original size:93 final size:93
Alignment explanation
Indices: 17216--17387 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
17206 CGCCCATAAG
*
17216 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
17280 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
17309 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
17374 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
17388 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:17382 original size:46 final size:46
Alignment explanation
Indices: 17209--17384 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
17199 TGTAACCCGC
* *
17209 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
17255 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
17305 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
17348 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
17385 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:24862 original size:93 final size:93
Alignment explanation
Indices: 24750--24921 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
24740 CGCCCATAAG
*
24750 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
24814 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
24843 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
24908 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
24922 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:24916 original size:46 final size:46
Alignment explanation
Indices: 24743--24918 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
24733 TGTAACCCGC
* *
24743 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
24789 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
24839 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
24882 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
24919 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.