Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1397
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: 27548
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4468 original size:15 final size:16
Alignment explanation
Indices: 4443--4473 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4433 AGTATGTCGG
4443 ATGATATATATTTTAA
1 ATGATATATATTTTAA
4459 ATGA-ATATATTTTAA
1 ATGATATATATTTTAA
4474 TTTTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATGATATATATTTTAA
Found at i:4489 original size:16 final size:17
Alignment explanation
Indices: 4448--4496 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
4438 GTCGGATGAT
*
4448 ATATATTTTAA-A-TGA
1 ATATATTTTAATATTTA
*
4463 ATATATTTTAATTTTTA
1 ATATATTTTAATATTTA
4480 ATAT-TTTTAATATTTA
1 ATATATTTTAATATTTA
4496 A
1 A
4497 ATAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.38
16 12 0.41
17 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATATTTTAATATTTA
Found at i:4499 original size:17 final size:17
Alignment explanation
Indices: 4462--4499 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4452 ATTTTAAATG
*
4462 AATATATTTTAATTTTT
1 AATATATTTTAATTTTA
4479 AATAT-TTTTAATATTTA
1 AATATATTTTAAT-TTTA
4496 AATA
1 AATA
4500 ATTATATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATATATTTTAATTTTA
Found at i:4530 original size:12 final size:13
Alignment explanation
Indices: 4515--4543 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4505 ATTCATAATT
4515 ATATTAAA-ATAA
1 ATATTAAATATAA
4527 ATATTAAATATAA
1 ATATTAAATATAA
4540 ATAT
1 ATAT
4544 GGTAATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:9069 original size:4 final size:4
Alignment explanation
Indices: 9060--9092 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
9050 ATACTTTCAC
*
9060 ATTA ATTA ATTG ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
9093 GAGAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:10054 original size:2 final size:2
Alignment explanation
Indices: 10043--10082 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
10033 ATTTTAACCA
10043 AT AT -T AT AT AT AT AT AT AT AT -T 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
10083 GTTATTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:10063 original size:17 final size:17
Alignment explanation
Indices: 10043--10080 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
10033 ATTTTAACCA
10043 ATATTATATATATATAT
1 ATATTATATATATATAT
10060 ATATTATATATATATAT
1 ATATTATATATATATAT
10077 ATAT
1 ATAT
10081 ATGTTATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATATATATAT
Found at i:13384 original size:32 final size:31
Alignment explanation
Indices: 13335--13407 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
13325 AAGCATTTAT
* *
13335 ATGTACTCACATTAGACACCTAAACACTGTTA
1 ATGTACTCATATCAGACACCTAAACACTG-TA
* *
13367 ATGTATTCATATCAGACAGCTAAACACTGTA
1 ATGTACTCATATCAGACACCTAAACACTGTA
13398 ATGTACTCAT
1 ATGTACTCAT
13408 TGTTTAGCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 11 0.31
32 25 0.69
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (31 bp):
ATGTACTCATATCAGACACCTAAACACTGTA
Found at i:24061 original size:16 final size:17
Alignment explanation
Indices: 24040--24149 Score: 79
Period size: 17 Copynumber: 6.6 Consensus size: 17
24030 CTCAACTCAA
24040 TAAATTTAATTTATA-T
1 TAAATTTAATTTATATT
* **
24056 TAAATTAAATTTA-AAA
1 TAAATTTAATTTATATT
24072 TAAA-TTAATTTATAATT
1 TAAATTTAATTTAT-ATT
24089 TAAA-TTAATTTA-ATT
1 TAAATTTAATTTATATT
*
24104 TAAATTATTATTTATA-T
1 TAAATT-TAATTTATATT
* ** *
24121 AAAAAATAATTTTTTATT
1 TAAATTTAA-TTTATATT
24139 TAAATTTAATT
1 TAAATTTAATT
24150 ATAAATATTA
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
15 15 0.21
16 19 0.26
17 30 0.42
18 8 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTTAATTTATATT
Found at i:24066 original size:21 final size:21
Alignment explanation
Indices: 24040--24109 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
24030 CTCAACTCAA
* *
24040 TAAATTTAATTTATATTAAAT
1 TAAATTTAAATTATATTAATT
* *
24061 TAAATTTAAAATAAATTAATT
1 TAAATTTAAATTATATTAATT
24082 TATAATTTAAATTA-ATTTAATT
1 TA-AATTTAAATTATA-TTAATT
24104 TAAATT
1 TAAATT
24110 ATTATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 24 0.57
22 18 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTTAAATTATATTAATT
Found at i:24106 original size:27 final size:28
Alignment explanation
Indices: 24042--24117 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 28
24032 CAACTCAATA
24042 AATTTAATTT-ATATTA-AA-TTAAATTT
1 AATTTAATTTAAT-TTATAATTTAAATTT
** *
24068 AAAATAAATTAATTTATAATTTAAA-TT
1 AATTTAATTTAATTTATAATTTAAATTT
* *
24095 AATTTAATTTAAATTATTATTTA
1 AATTTAATTTAATTTATAATTTA
24118 TATAAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
26 10 0.26
27 24 0.62
28 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTTAATTTAATTTATAATTTAAATTT
Found at i:24169 original size:14 final size:15
Alignment explanation
Indices: 24147--24180 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
24137 TTTAAATTTA
24147 ATTATAAATATTAAT
1 ATTATAAATATTAAT
*
24162 ATTA-AAATTTTAAT
1 ATTATAAATATTAAT
24176 ATTAT
1 ATTAT
24181 TTAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAATATTAAT
Found at i:24211 original size:30 final size:31
Alignment explanation
Indices: 24137--24219 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 31
24127 TAATTTTTTA
* *
24137 TTTAAATTTAATTATAAATATTAATATTAAAAT
1 TTTAAATTT-ATT-TAAATAATAATAATAAAAT
*
24170 TTT-AATATTATTTAAATAATAA-AATAAATT
1 TTTAAAT-TTATTTAAATAATAATAATAAAAT
*
24200 TTTAAATTTATTTAAGTAAT
1 TTTAAATTTATTTAAATAAT
24220 TCAATCTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 21 0.48
31 12 0.27
32 6 0.14
33 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
TTTAAATTTATTTAAATAATAATAATAAAAT
Found at i:24566 original size:23 final size:24
Alignment explanation
Indices: 24540--24594 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
24530 TAATATTTAA
24540 ATTTAAATATTTATAA-TT-TTTT-T
1 ATTTAAA-A-TTATAATTTCTTTTGT
*
24563 ATTTCAAATTATAATTTCTTTTGT
1 ATTTAAAATTATAATTTCTTTTGT
24587 ATTTAAAA
1 ATTTAAAA
24595 AAAATTAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.22
22 3 0.11
23 10 0.37
24 8 0.30
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTAAAATTATAATTTCTTTTGT
Found at i:25080 original size:26 final size:25
Alignment explanation
Indices: 25002--25081 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 25
24992 AATTAAAAAT
*
25002 AATATTTTTTTATATTTAATAATT-
1 AATAATTTTTTATATTTAATAATTA
25026 AA-AATTTTTTATATTTAATAAATCATA
1 AATAATTTTTTATATTTAAT-AAT--TA
25053 AATAATTTTAATT-TATTTAATAATTA
1 AATAATTTT--TTATATTTAATAATTA
25079 AAT
1 AAT
25082 TTAATTACAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
23 16 0.33
24 5 0.10
26 6 0.12
27 2 0.04
28 9 0.19
29 8 0.17
30 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
AATAATTTTTTATATTTAATAATTA
Found at i:25131 original size:17 final size:17
Alignment explanation
Indices: 25098--25131 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25088 ACAAATATAA
*
25098 AAAATTTAAAATTAAAT
1 AAAATTTAAAATGAAAT
*
25115 AAAATTTATAATGAAAT
1 AAAATTTAAAATGAAAT
25132 TATAAAAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATTTAAAATGAAAT
Found at i:26710 original size:51 final size:51
Alignment explanation
Indices: 26618--26736 Score: 150
Period size: 51 Copynumber: 2.4 Consensus size: 51
26608 ACTATCCTTT
* * * * *
26618 ACCAATCTTTGAC-AATAGAGAGAGGTGGTCGTAATTGTTGACGATTCTTC
1 ACCAACCTTTGACAAATGGAGAGAGGTGGCCATAATTATTGACGATTCTTC
* * *
26668 ACTAACTTTTGACAAATGGAGAGAGGTGGCCATTATTATTGACGATTCTTC
1 ACCAACCTTTGACAAATGGAGAGAGGTGGCCATAATTATTGACGATTCTTC
*
26719 ACCAACCTTTAACAAATG
1 ACCAACCTTTGACAAATG
26737 TGGCCATAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 10 0.18
51 47 0.82
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (51 bp):
ACCAACCTTTGACAAATGGAGAGAGGTGGCCATAATTATTGACGATTCTTC
Done.