Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold704
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: 26163
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:142 original size:40 final size:39
Alignment explanation
Indices: 89--205 Score: 173
Period size: 40 Copynumber: 2.9 Consensus size: 39
79 AAGCACTTGG
*
89 AAAATGGCTTCAGATAAAAGCACTTGAAAAATGAAATTGA
1 AAAATGGCTTCAGA-AAAAGTACTTGAAAAATGAAATTGA
129 AAAATGGCTTCAG-AAAAGTTTACTTGAAAAATGAAATTGA
1 AAAATGGCTTCAGAAAAAG--TACTTGAAAAATGAAATTGA
*
169 AAAATGGCTTCAGAAAAATTTACTTGAAAAATGAAAT
1 AAAATGGCTTCAGAAAAA-GTACTTGAAAAATGAAAT
206 ATCCGCATGT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
38 5 0.07
40 62 0.87
41 4 0.06
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.26
Consensus pattern (39 bp):
AAAATGGCTTCAGAAAAAGTACTTGAAAAATGAAATTGA
Found at i:3953 original size:18 final size:17
Alignment explanation
Indices: 3930--3983 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
3920 TATATTTTAT
3930 AATTTAATAAAAAAATTA
1 AATTTAA-AAAAAAATTA
3948 AATTTAAAAAAATAA--A
1 AATTTAAAAAAA-AATTA
*
3964 AATATAAAAAAAAATTA
1 AATTTAAAAAAAAATTA
3981 AAT
1 AAT
3984 AAACTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.06
16 12 0.38
17 9 0.28
18 9 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATTTAAAAAAAAATTA
Found at i:3959 original size:16 final size:16
Alignment explanation
Indices: 3938--3984 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
3928 ATAATTTAAT
*
3938 AAAAAAATTAAAT-TT
1 AAAAAAATTAAATATA
*
3953 AAAAAAATAAAAATATAA
1 AAAAAAAT-TAAATAT-A
3971 AAAAAAATTAAATA
1 AAAAAAATTAAATA
3985 AACTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 6 0.23
18 8 0.31
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAATTAAATATA
Found at i:8621 original size:2 final size:2
Alignment explanation
Indices: 8616--8702 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
8606 AAATTTTAAA
* *
8616 AT AT AT AT TT AT GT AT AT -T AT AT -T AT AT -T A- AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
8652 TT AT TT AT AT AT A- AT AT -T AA AT AT A- AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8689 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
8703 GTGTTTAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
1 11 0.17
2 54 0.83
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (2 bp):
AT
Found at i:8652 original size:27 final size:28
Alignment explanation
Indices: 8621--8702 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
8611 TTAAAATATA
*
8621 TATTTATGTATATTATATTATAT-TAAT
1 TATTTATATATATTATATTATATATAAT
* *
8648 TATTTTATTTATATATAATATTAAATATAAT
1 TA-TTTA--TATATATTATATTATATATAAT
8679 TATATTATATATA-TATA-TATATAT
1 TAT-TTATATATATTATATTATATAT
8703 GTGTTTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
27 8 0.18
28 7 0.16
29 6 0.13
30 15 0.33
31 9 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTTATATATATTATATTATATATAAT
Found at i:8668 original size:25 final size:27
Alignment explanation
Indices: 8629--8696 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
8619 TATATTTATG
* *
8629 TATATTATAT-T-ATATTAATTAT-TT
1 TATATTATATATAATATTAAATATAAT
8653 TAT-TTATATATAATATTAAATATAAT
1 TATATTATATATAATATTAAATATAAT
8679 TATATTATATATATATAT
1 TATATTATATATA-ATAT
8697 ATATATGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 6 0.16
24 4 0.11
25 10 0.27
26 4 0.11
27 9 0.24
28 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TATATTATATATAATATTAAATATAAT
Found at i:8669 original size:18 final size:19
Alignment explanation
Indices: 8619--8666 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
8609 TTTTAAAATA
* *
8619 TATATTTATGTATATTATAT
1 TATATTAAT-TATTTTATAT
8639 TATATTAATTATTTTAT-T
1 TATATTAATTATTTTATAT
8657 TATATATAAT
1 TATAT-TAAT
8667 ATTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.24
19 11 0.44
20 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATTAATTATTTTATAT
Found at i:8690 original size:52 final size:56
Alignment explanation
Indices: 8537--8702 Score: 155
Period size: 56 Copynumber: 2.9 Consensus size: 56
8527 AAATTTATGC
* *
8537 ATTAATATTATAT-TATATTTAAAATATTATATTTATATAAATT-T-TGATATATTAATA
1 ATTAAT-TTATATAAATA-TTAAAATA-TATATTTATATATATTATAT-ATATATTAATA
* *
8594 ATTAATTTATATAAATTTTAAAATATATATTTATGTATATTATAT-TATATTAATTA
1 ATTAATTTATATAAATATTAAAATATATATTTATATATATTATATATATATTAA-TA
* *
8650 TTTTATTTATATATAATATT-AAATATA-ATTATATTATATATATATATATATAT
1 ATTAATTTATATA-AATATTAAAATATATATT-TA-TATATAT-TATATATATAT
8703 GTGTTTAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
55 25 0.27
56 37 0.40
57 20 0.22
58 5 0.05
59 5 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (56 bp):
ATTAATTTATATAAATATTAAAATATATATTTATATATATTATATATATATTAATA
Found at i:8997 original size:23 final size:21
Alignment explanation
Indices: 8971--9063 Score: 57
Period size: 23 Copynumber: 4.2 Consensus size: 21
8961 TAAAAAAAAT
* *
8971 TAAATATATTATTAACATATATA
1 TAAATAAATAATTAA-AT-TATA
8994 TAAATAAATAATTAAATTATA
1 TAAATAAATAATTAAATTATA
*
9015 TTTATATTAAA-AATTAAATTAGTA
1 --TA-AATAAATAATTAAATTA-TA
*
9039 -AAATAAA-AATAATAAATTATT
1 TAAATAAATAAT--TAAATTATA
9060 TAAA
1 TAAA
9064 ATTTAAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
20 8 0.14
21 6 0.10
22 12 0.21
23 25 0.43
24 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
TAAATAAATAATTAAATTATA
Found at i:9681 original size:30 final size:31
Alignment explanation
Indices: 9630--9722 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
9620 TATTTTTATT
*
9630 AAAAAATTTTAATAATTTAATATAATAAATA
1 AAAAAATTTTAATAATTTAATAAAATAAATA
*
9661 AAAAAATTTT-AT-TTTATAATAAAATAAATA
1 AAAAAATTTTAATAATT-TAATAAAATAAATA
* * * * *
9691 ATAAGATATTTAATTA-TTCATAAATTAAATA
1 AAAAAAT-TTTAATAATTTAATAAAATAAATA
9722 A
1 A
9723 CTTTAAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 2 0.04
30 20 0.39
31 26 0.51
32 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAAAATTTTAATAATTTAATAAAATAAATA
Found at i:14934 original size:2 final size:2
Alignment explanation
Indices: 14929--14963 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
14919 GTGTGTGTGT
*
14929 TC TC TC TC TC -C TT 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 TC TC
14964 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:23021 original size:30 final size:32
Alignment explanation
Indices: 22957--23040 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 32
22947 TCATAACTTA
* * *
22957 AAATAAACTATTAA-TTTTTAATTTTTTAATT
1 AAATAAAATCTTAATTTTTTAATTTTATAATT
*
22988 AAAT-GAATACTTAATTTTTTAA-TTTAT-ATT
1 AAATAAAAT-CTTAATTTTTTAATTTTATAATT
23018 AAATAAAATCTTAATTTGTTTAA
1 AAATAAAATCTTAATTT-TTTAA
23041 AATAAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 17 0.39
31 20 0.45
32 7 0.16
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (32 bp):
AAATAAAATCTTAATTTTTTAATTTTATAATT
Found at i:24545 original size:2 final size:2
Alignment explanation
Indices: 24540--24567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24530 CCCCCCCCCC
24540 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
24568 TCTTCTTCTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:25976 original size:16 final size:16
Alignment explanation
Indices: 25950--26048 Score: 53
Period size: 16 Copynumber: 5.9 Consensus size: 16
25940 TCAAGTGATC
25950 TTATA-TTTATTTAAA
1 TTATATTTTATTTAAA
25965 TTATATTTTATTT--A
1 TTATATTTTATTTAAA
* *
25979 TTATCAATTAATTTTAAA
1 TTAT-ATTTTA-TTTAAA
*
25997 TTAAATATTTAATATTAATTAA
1 TT--ATATTT--TATT--TAAA
26019 TTATATTATT-TTTAAA
1 TTATATT-TTATTTAAA
*
26035 TTATATATTATTTA
1 TTATATTTTATTTA
26049 TATTTTATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 25
0.67 0.07 0.26
Matches are distributed among these distances:
14 5 0.08
15 11 0.17
16 23 0.36
18 5 0.08
19 4 0.06
20 9 0.14
21 2 0.03
22 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATTTTATTTAAA
Found at i:25978 original size:20 final size:20
Alignment explanation
Indices: 25953--25994 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
25943 AGTGATCTTA
25953 TATTTATT-TAAATTATATTT
1 TATTTATTATAAATTA-ATTT
*
25973 TATTTATTATCAATTAATTT
1 TATTTATTATAAATTAATTT
25993 TA
1 TA
25995 AATTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTATTATAAATTAATTT
Found at i:26057 original size:16 final size:16
Alignment explanation
Indices: 26008--26057 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
25998 TAAATATTTA
*
26008 ATATTAATTA-ATTAT
1 ATATTATTTATATTAT
*
26023 ATTATT-TTTAAATTAT
1 A-TATTATTTATATTAT
*
26039 ATATTATTTATATTTT
1 ATATTATTTATATTAT
26055 ATA
1 ATA
26058 AAATTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTTATATTAT
Done.