Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3665
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: 37453
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:944 original size:29 final size:29
Alignment explanation
Indices: 910--969 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
900 ATGTATTAGT
* *
910 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
939 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
968 TT
1 TT
970 TTCTGTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:6289 original size:20 final size:19
Alignment explanation
Indices: 6266--6330 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
6256 AAGCTCAAAC
6266 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
6286 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
6306 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
6326 GAGCT
1 GAGCT
6331 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:11591 original size:29 final size:29
Alignment explanation
Indices: 11557--11629 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
11547 ATGTATTAGT
* *
11557 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
11586 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
11615 TTAGGACATATTTAA
1 TTAGGACATATTTAA
11630 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:13733 original size:14 final size:14
Alignment explanation
Indices: 13714--13755 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
13704 TAGTTTAATG
13714 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
13728 ATTTTTATTTATTT
1 ATTTTTATTTTTTT
13742 ATTTCTTAGTTTTT
1 ATTT-TTA-TTTTT
13756 AAGTTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
15 3 0.12
16 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:14322 original size:14 final size:15
Alignment explanation
Indices: 14303--14339 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
14293 TTATTGATGC
14303 TTAAATTAAG-TTCT
1 TTAAATTAAGCTTCT
*
14317 TTAAATTATGCTTCT
1 TTAAATTAAGCTTCT
14332 TT-AATTAA
1 TTAAATTAA
14340 ACTAGTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAAATTAAGCTTCT
Found at i:15252 original size:12 final size:12
Alignment explanation
Indices: 15235--15289 Score: 103
Period size: 12 Copynumber: 4.7 Consensus size: 12
15225 TAGTTTCTTC
15235 AAAAAAAATTCA
1 AAAAAAAATTCA
15247 AAAAAAAATTCA
1 AAAAAAAATTCA
15259 AAAAAAAATTC-
1 AAAAAAAATTCA
15270 AAAAAAAATTCA
1 AAAAAAAATTCA
15282 AAAAAAAA
1 AAAAAAAA
15290 ATTGGTTTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.26
12 31 0.74
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:15292 original size:24 final size:24
Alignment explanation
Indices: 15235--15289 Score: 103
Period size: 23 Copynumber: 2.3 Consensus size: 24
15225 TAGTTTCTTC
15235 AAAAAAAATTCAAAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAAATTCA
15259 AAAAAAAATTC-AAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAAATTCA
15282 AAAAAAAA
1 AAAAAAAA
15290 ATTGGTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (24 bp):
AAAAAAAATTCAAAAAAAAATTCA
Found at i:15352 original size:16 final size:17
Alignment explanation
Indices: 15331--15368 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
15321 TATCAAGTTG
15331 AAAAAAAA-TTCGTGAA
1 AAAAAAAATTTCGTGAA
15347 AAAAAAAATTTCGTGAA
1 AAAAAAAATTTCGTGAA
15364 AAAAA
1 AAAAA
15369 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAAAAAATTTCGTGAA
Found at i:16939 original size:20 final size:19
Alignment explanation
Indices: 16914--16968 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
16904 TGTGGTTCAA
*
16914 CTCATTCGAGCTCAAGTTAG
1 CTCATTC-AGCTCAAGTCAG
16934 CTCATTCATGCTCAAGTCAG
1 CTCATTCA-GCTCAAGTCAG
16954 CTCATTCAAGCTCAA
1 CTCATTC-AGCTCAA
16969 TTTAACTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (19 bp):
CTCATTCAGCTCAAGTCAG
Found at i:18979 original size:11 final size:11
Alignment explanation
Indices: 18965--19008 Score: 79
Period size: 11 Copynumber: 3.9 Consensus size: 11
18955 AAAAAAAAGG
18965 AAAAAAAATTC
1 AAAAAAAATTC
18976 AAAAAAAAATTC
1 -AAAAAAAATTC
18988 AAAAAAAATTC
1 AAAAAAAATTC
18999 AAAAAAAATT
1 AAAAAAAATT
19009 TGTATTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:18980 original size:12 final size:12
Alignment explanation
Indices: 18965--19006 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
18955 AAAAAAAAGG
18965 AAAAAAAATTCA
1 AAAAAAAATTCA
18977 AAAAAAAATTC-
1 AAAAAAAATTCA
18988 AAAAAAAATTCA
1 AAAAAAAATTCA
19000 AAAAAAA
1 AAAAAAA
19007 TTTGTATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:21554 original size:20 final size:20
Alignment explanation
Indices: 21529--21583 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21519 TGTGGTTCAA
*
21529 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
21549 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
21569 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
21584 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:23610 original size:12 final size:11
Alignment explanation
Indices: 23578--23607 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
23568 AAAAAAAAGG
23578 AAAAAAAATTC
1 AAAAAAAATTC
23589 AAAAAAAATTC
1 AAAAAAAATTC
23600 AAAAAAAA
1 AAAAAAAA
23608 ATTTTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:26134 original size:20 final size:20
Alignment explanation
Indices: 26109--26163 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
26099 TGTGGTTCAA
*
26109 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
26129 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
26149 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
26164 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:37217 original size:23 final size:23
Alignment explanation
Indices: 37191--37251 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
37181 GAATATTGAC
37191 ATAAAAATTTAAACT-AATAATAA
1 ATAAAAATTTAAACTAAATAA-AA
*
37214 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
37236 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
37252 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 16 0.53
24 3 0.10
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:37218 original size:4 final size:4
Alignment explanation
Indices: 37209--37234 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
37199 TTAAACTAAT
37209 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
37235 AATAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Done.