Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1626
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: 39591
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4113 original size:1 final size:1
Alignment explanation
Indices: 4107--4131 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4097 CAACAACCGC
4107 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
4132 AATGGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:5391 original size:2 final size:2
Alignment explanation
Indices: 5384--5416 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5374 GATAGGGAGG
5384 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5417 CTGACCTCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5647 original size:11 final size:12
Alignment explanation
Indices: 5630--5658 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5620 AAAGTCGCCC
5630 CTTGCTTTTAAT
1 CTTGCTTTTAAT
5642 -TTGCTTTTAAT
1 CTTGCTTTTAAT
5653 CTTGCT
1 CTTGCT
5659 CAGGAAGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (12 bp):
CTTGCTTTTAAT
Found at i:6336 original size:21 final size:21
Alignment explanation
Indices: 6310--6349 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6300 ATTAAAAAAT
6310 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
6331 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
6350 AATAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:6360 original size:23 final size:21
Alignment explanation
Indices: 6311--6361 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
6301 TTAAAAAATT
*
6311 ATTTTATATTAATATTTATAT
1 ATTTTATATTAATATTTATAA
6332 ATTTTATAATTAA-ATTTAAATAA
1 ATTTTAT-ATTAATATTT--ATAA
6355 ATTTTAT
1 ATTTTAT
6362 TAAATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 5 0.19
23 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTATATTAATATTTATAA
Found at i:8509 original size:43 final size:43
Alignment explanation
Indices: 8448--8535 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
8438 ACTTCAAATG
8448 TGAAACATATATTAAAATCACATACAACCATAAAATTCTAAGC
1 TGAAACATATATTAAAATCACATACAACCATAAAATTCTAAGC
8491 TGAAACATATATTAAAATCACATACAACCATAAAATTCTAAGC
1 TGAAACATATATTAAAATCACATACAACCATAAAATTCTAAGC
8534 TG
1 TG
8536 GGACACCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (43 bp):
TGAAACATATATTAAAATCACATACAACCATAAAATTCTAAGC
Found at i:16332 original size:21 final size:21
Alignment explanation
Indices: 16308--16359 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
16298 GAACTAGAGG
*
16308 AGAAAATG-AATATGTTGGAAA
1 AGAAAATGAAATA-GTTGCAAA
16329 AGAAAA-GAAATGAGTTGCAAA
1 AGAAAATGAAAT-AGTTGCAAA
16350 ATGAAAATGA
1 A-GAAAATGA
16360 TGAATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 17 0.65
22 6 0.23
23 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (21 bp):
AGAAAATGAAATAGTTGCAAA
Found at i:17903 original size:13 final size:13
Alignment explanation
Indices: 17876--17914 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
17866 AAGAAAGTTA
* *
17876 TATCAATACACTG
1 TATCGATACATTG
*
17889 TATCGATCCATTG
1 TATCGATACATTG
17902 TATCGATACATTG
1 TATCGATACATTG
17915 CTTTGGTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:21396 original size:20 final size:20
Alignment explanation
Indices: 21354--21406 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
21344 TTTTACAATT
* *
21354 TGTATCAATACAACAAGTTAA
1 TGTATCGATAC-ACAAGTAAA
*
21375 TGTATCGATACATAAGTAAA
1 TGTATCGATACACAAGTAAA
*
21395 TGTATTGATACA
1 TGTATCGATACA
21407 GGACCTTGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
TGTATCGATACACAAGTAAA
Found at i:21558 original size:52 final size:52
Alignment explanation
Indices: 21441--21560 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
21431 ATTCTGAAAA
* * * *
21441 AAATGTATCGATACA-TTTTTATTGTATCGATACATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATTTTTTATTGTATCAATACATTCTAGGTTTTTAACCC
* ** * *
21492 AAATGCATTAATACATTTTTTATTGTATCAATATATTCTAGGTTTTTAACTC
1 AAATGTATCGATACATTTTTTATTGTATCAATACATTCTAGGTTTTTAACCC
*
21544 AAGTGTATCGATACATT
1 AAATGTATCGATACATT
21561 CTTCAATGTA
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
51 12 0.22
52 43 0.78
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTTATTGTATCAATACATTCTAGGTTTTTAACCC
Found at i:29947 original size:21 final size:21
Alignment explanation
Indices: 29923--29999 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
29913 AAAATTTCCA
29923 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
29944 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
29965 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
29986 AATGTATCGATACA
1 AATGTATCGATACA
30000 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:30059 original size:19 final size:19
Alignment explanation
Indices: 30035--30102 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
30025 AATTCAACAG
30035 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
30054 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
30069 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
30086 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
30103 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:30073 original size:32 final size:32
Alignment explanation
Indices: 30037--30099 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
30027 TTCAACAGTT
*
30037 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
30069 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
30100 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:30074 original size:13 final size:13
Alignment explanation
Indices: 30056--30080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30046 ACATAAGTTT
30056 TGTATCGATACAA
1 TGTATCGATACAA
30069 TGTATCGATACA
1 TGTATCGATACA
30081 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:30179 original size:33 final size:33
Alignment explanation
Indices: 30122--30188 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
30112 GCCAAGGAAA
*** *
30122 TGTATCGATACATTTTTCTATGTATTGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
30155 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
30188 T
1 T
30189 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:32585 original size:51 final size:53
Alignment explanation
Indices: 32521--32651 Score: 178
Period size: 51 Copynumber: 2.5 Consensus size: 53
32511 AGTTTCTCAA
* * * *
32521 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
32572 TT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
32626 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
32652 CCCGTTAATC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
50 2 0.03
51 34 0.49
53 9 0.13
54 21 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:32665 original size:27 final size:28
Alignment explanation
Indices: 32635--32710 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
32625 TTTCTTCACA
32635 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
32662 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
32690 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
32711 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:32768 original size:51 final size:51
Alignment explanation
Indices: 32693--32914 Score: 212
Period size: 51 Copynumber: 4.4 Consensus size: 51
32683 TTATTTCTGA
* * *
32693 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCGATTTTTCATAATC
* * * * ** *
32744 GGGGATACTCCAACCTCGGTTTTATTGCTAAAACATTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCGATTTTT-CATAATC
* * * * * ****
32796 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACA-CCAATTTTCCTCCGA
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCGATTTTTCATAATC
* * * *
32846 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCGATTTCTCATAATT
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCGATTTTTCATAATC
*
32897 AGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
32915 TTATTTCCGA
Statistics
Matches: 135, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
50 32 0.24
51 66 0.49
52 37 0.27
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCGATTTTTCATAATC
Done.