Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold544
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: 110692
ACGTcount: A:0.16, C:0.08, G:0.09, T:0.16
Warning! 55171 characters in sequence are not A, C, G, or T
Found at i:2717 original size:20 final size:20
Alignment explanation
Indices: 2683--2722 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2673 TAGCTCAACG
* *
2683 AGCTCATTTTTAGCTCATTT
1 AGCTCATCTTAAGCTCATTT
*
2703 AGCTCATCTTAAGCTTATTT
1 AGCTCATCTTAAGCTCATTT
2723 TAGTTTGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (20 bp):
AGCTCATCTTAAGCTCATTT
Found at i:18703 original size:16 final size:15
Alignment explanation
Indices: 18677--18706 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18667 CTTCAAACCA
18677 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
18692 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
18707 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:19201 original size:6 final size:6
Alignment explanation
Indices: 19190--19238 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
19180 TCGCTCGCAC
* ** *
19190 TCTTTT TCTTTT TCTATT TC-TTT TCACTT TCTTTT TGTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
19237 TC
1 TC
19239 ACATGCTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (6 bp):
TCTTTT
Found at i:33644 original size:24 final size:23
Alignment explanation
Indices: 33590--33645 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
33580 GATTAATTAA
**
33590 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
33613 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
33637 GAAATGGTA
1 GAAATGGTA
33646 AGGNNNNNNN
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:34617 original size:30 final size:30
Alignment explanation
Indices: 34559--34617 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
34549 TTAGAAATGT
* *
34559 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
34589 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
34618 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:35298 original size:50 final size:52
Alignment explanation
Indices: 35172--35298 Score: 127
Period size: 50 Copynumber: 2.5 Consensus size: 52
35162 ATGAACAAAT
* *
35172 GAGTTACTTAATGCA-AGACTTAATTTAAAGATGCAGACTTAAACTAACATAA
1 GAGTTACATAATGCATA-ACTTTATTTAAAGATGCAGACTTAAACTAACATAA
** * * * * *
35224 GAGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCAT-G
1 GAGTTACATAATGCATAACTTTATTTAAAGATGCAGACTTAAACTAACATAA
35273 GAAGTTACATAATGCATAACTTTATT
1 G-AGTTACATAATGCATAACTTTATT
35299 AAATGCAGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
49 1 0.02
50 29 0.48
51 11 0.18
52 20 0.33
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (52 bp):
GAGTTACATAATGCATAACTTTATTTAAAGATGCAGACTTAAACTAACATAA
Found at i:35384 original size:20 final size:19
Alignment explanation
Indices: 35343--35384 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
35333 AAAAATATGT
*
35343 AAACTTATTAATTTAAATA
1 AAACTTATTAATTTAAAAA
35362 AAACTATATTGAA-TTAAAAA
1 AAACT-TATT-AATTTAAAAA
35382 AAA
1 AAA
35385 GTCCTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 13 0.65
21 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
AAACTTATTAATTTAAAAA
Found at i:37916 original size:14 final size:13
Alignment explanation
Indices: 37897--37945 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
37887 CAAGTTGTGA
37897 AAAAAAAAGTTTTG
1 AAAAAAAA-TTTTG
*
37911 AAAAAAAAATTTG
1 AAAAAAAATTTTG
*
37924 AAAAAAAAATTGTG
1 -AAAAAAAATTTTG
37938 AAAAAAAA
1 AAAAAAAA
37946 AAGAGAGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
AAAAAAAATTTTG
Found at i:37947 original size:15 final size:14
Alignment explanation
Indices: 37891--37946 Score: 87
Period size: 13 Copynumber: 4.0 Consensus size: 14
37881 GGATATCAAG
37891 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
37905 GTTTTGAAAAAAAAA
1 -TTGTGAAAAAAAAA
37920 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
37933 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
37947 AGAGAGCTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 13 0.33
14 13 0.33
15 13 0.33
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:44007 original size:11 final size:10
Alignment explanation
Indices: 43991--44038 Score: 62
Period size: 11 Copynumber: 4.7 Consensus size: 10
43981 GTAGGTTCGT
43991 AAAAAAATTG
1 AAAAAAATTG
44001 AAAAAAAATTTG
1 -AAAAAAA-TTG
44013 AAAAAAATT-
1 AAAAAAATTG
*
44022 AAAAAAATCG
1 AAAAAAATTG
44032 AAAAAAA
1 AAAAAAA
44039 GAGATATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 8 0.24
10 9 0.26
11 14 0.41
12 3 0.09
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:60083 original size:85 final size:86
Alignment explanation
Indices: 59968--60124 Score: 280
Period size: 85 Copynumber: 1.8 Consensus size: 86
59958 GTAATAAAGA
*
59968 TAAAATATAAGATATTCGGTGAGAATGGATAAATGAGCTTAAACACCAGAAACGATTCAACACTA
1 TAAAATATAAGATAGTCGGTGAGAATGGATAAATGAGCTTAAACACCAGAAACGATTCAACACTA
60033 AAAAGTGATATTATAGTTGGG
66 AAAAGTGATATTATAGTTGGG
* *
60054 TAAAATCTAGGATAGTCGGTG-GAATGGATAAATGAGCTTAAACACCAGAAACGATTCAACACTA
1 TAAAATATAAGATAGTCGGTGAGAATGGATAAATGAGCTTAAACACCAGAAACGATTCAACACTA
60118 AAAAGTG
66 AAAAGTG
60125 TCACCCCGAT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
85 50 0.74
86 18 0.26
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (86 bp):
TAAAATATAAGATAGTCGGTGAGAATGGATAAATGAGCTTAAACACCAGAAACGATTCAACACTA
AAAAGTGATATTATAGTTGGG
Found at i:62930 original size:21 final size:21
Alignment explanation
Indices: 62904--62945 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62894 AAAATTGAAA
**
62904 AAGAAAATGAGTTAGAAAAAG
1 AAGAAAATGAGCGAGAAAAAG
*
62925 AAGAAATTGAGCGAGAAAAAG
1 AAGAAAATGAGCGAGAAAAAG
62946 CTAGAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.26, T:0.12
Consensus pattern (21 bp):
AAGAAAATGAGCGAGAAAAAG
Done.