Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2274
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: 36161
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:342 original size:13 final size:13
Alignment explanation
Indices: 302--362 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
292 ATATAGAATA
302 TTTAAAATTATAT
1 TTTAAAATTATAT
*
315 CTTTTAAA--A-AT
1 -TTTAAAATTATAT
*
326 TTTAATATTATAT
1 TTTAAAATTATAT
339 TTTAAAATTATATCT
1 TTTAAAATTATA--T
354 TTTAAAATT
1 TTTAAAATT
363 TTTTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 5 0.13
11 2 0.05
12 2 0.05
13 13 0.34
14 6 0.16
15 10 0.26
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAAATTATAT
Found at i:344 original size:22 final size:23
Alignment explanation
Indices: 302--345 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
292 ATATAGAATA
302 TTTAAAATTATATCTTTTAAAAAT
1 TTTAAAATTATA-CTTTTAAAAAT
*
326 TTTAATATTATA-TTTTAAAA
1 TTTAAAATTATACTTTTAAAA
346 TTATATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAATTATACTTTTAAAAAT
Found at i:1590 original size:17 final size:16
Alignment explanation
Indices: 1551--1594 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1541 TACATTTATT
**
1551 TTTTATATTTTTTGAA
1 TTTTATATTTTTAAAA
1567 TTATTATATTTTTAAAA
1 TT-TTATATTTTTAAAA
1584 TATTTATATTT
1 T-TTTATATTT
1595 GATATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTATATTTTTAAAA
Found at i:2642 original size:19 final size:18
Alignment explanation
Indices: 2618--2654 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2608 AAAATAAAAA
2618 AATCAAAATCATTAATTTT
1 AATC-AAATCATTAATTTT
*
2637 AATCAATTCATTAATTTT
1 AATCAAATCATTAATTTT
2655 TGTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
AATCAAATCATTAATTTT
Found at i:2893 original size:53 final size:54
Alignment explanation
Indices: 2822--2924 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
2812 TGATACCTCG
* * *
2822 TAAAAAGTAATAAGAACATAATCTAAATATATGAATGCATTAAAATATATATTA
1 TAAAAAGTAATAAAAACATAATCTAAATATATAAATACATTAAAATATATATTA
*
2876 TAAAAA-TAATAAAAACATGATCTAAATATATAAATACATTAAAATATAT
1 TAAAAAGTAATAAAAACATAATCTAAATATATAAATACATTAAAATATAT
2925 GTAATTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 39 0.87
54 6 0.13
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (54 bp):
TAAAAAGTAATAAAAACATAATCTAAATATATAAATACATTAAAATATATATTA
Found at i:2949 original size:32 final size:33
Alignment explanation
Indices: 2898--2961 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
2888 AAACATGATC
*
2898 TAAATATATAAATACATTAAAATATATGTAATT
1 TAAATATATAAATACATTAAAATATATATAATT
* * *
2931 TAAAT-TATTAATATATTAAAATTTATATAAT
1 TAAATATATAAATACATTAAAATATATATAAT
2962 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (33 bp):
TAAATATATAAATACATTAAAATATATATAATT
Found at i:2963 original size:19 final size:19
Alignment explanation
Indices: 2935--2985 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2925 GTAATTTAAA
2935 TTAT-TAATATATTAAAAT
1 TTATATAATATATTAAAAT
2953 TTATATAATATATTAAAAT
1 TTATATAATATATTAAAAT
2972 TTATATAAATATAT
1 TTATAT-AATATAT
2986 ATTATCCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.13
19 20 0.65
20 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATATAATATATTAAAAT
Found at i:3703 original size:28 final size:28
Alignment explanation
Indices: 3671--3729 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
3661 ATTATAGTTC
* *
3671 GATCGACAAATAAAATTTATTTGTAAAA
1 GATCGACAAACAAAATTTACTTGTAAAA
*
3699 GATCGATAAACAAAATTTACTTGTAAAA
1 GATCGACAAACAAAATTTACTTGTAAAA
3727 GAT
1 GAT
3730 AAGTTAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (28 bp):
GATCGACAAACAAAATTTACTTGTAAAA
Found at i:7911 original size:11 final size:10
Alignment explanation
Indices: 7884--7914 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
7874 TATTATTGTT
7884 AATATTTTTA
1 AATATTTTTA
7894 AATATTTTTA
1 AATATTTTTA
*
7904 AATAATTTTA
1 AATATTTTTA
7914 A
1 A
7915 TGATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATATTTTTA
Found at i:12192 original size:2 final size:2
Alignment explanation
Indices: 12185--12216 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12175 TATTTGGGAA
12185 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12217 CCCTTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12928 original size:2 final size:2
Alignment explanation
Indices: 12923--12951 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12913 CTTTTGTTTC
12923 CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12952 GTTTGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:32920 original size:103 final size:105
Alignment explanation
Indices: 32802--33020 Score: 300
Period size: 103 Copynumber: 2.1 Consensus size: 105
32792 GGGGGGGGGG
* **
32802 GAGAGAGAAACTAGCTATTGGGATTAGTGTAGTAAAAAGAATTGCAAGTGTAAT-ATTCTCAAAC
1 GAGAGAGAGACTAGCTATTGGGATTAGTGTAGTAAAAAGAATTGCAAGTACAATGA-TCTCAAAC
* *
32866 AA-CCATTATAAGAGTAAAGGTTGTA-CAGAGAGAGAGAGA
65 AATCAATTATAAGAGTAAAGATTGTAGCAGAGAGAGAGAGA
* * * *
32905 GAGAGAGAGATTAGCTATTGGGATTATTGTAGTAAAAAGAATTGCAGGTACAATGATCTCAGACA
1 GAGAGAGAGACTAGCTATTGGGATTAGTGTAGTAAAAAGAATTGCAAGTACAATGATCTCAAACA
* *
32970 ATGAATTATAAGAGTAAAGATTTTAGTCAGAGAGAGAGAGA
66 ATCAATTATAAGAGTAAAGATTGTAG-CAGAGAGAGAGAGA
33011 GAGAGAGAGA
1 GAGAGAGAGA
33021 GAGAGATAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
103 57 0.56
104 20 0.20
106 24 0.24
ACGTcount: A:0.42, C:0.07, G:0.27, T:0.23
Consensus pattern (105 bp):
GAGAGAGAGACTAGCTATTGGGATTAGTGTAGTAAAAAGAATTGCAAGTACAATGATCTCAAACA
ATCAATTATAAGAGTAAAGATTGTAGCAGAGAGAGAGAGA
Found at i:33005 original size:2 final size:2
Alignment explanation
Indices: 32998--33026 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32988 GATTTTAGTC
32998 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
33027 TAAACTAGCC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33877 original size:2 final size:2
Alignment explanation
Indices: 33870--33928 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
33860 AACCTTCAAA
* *
33870 AT AT AT AT AT TT AT AT AT TT 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 AT AT AT AT AT AT AT
33912 AT AT AT AT GAT AT AT AT
1 AT AT AT AT -AT AT AT AT
33929 TCATATTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Done.