Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3802
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: 50801
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:4261 original size:29 final size:31
Alignment explanation
Indices: 4224--4303 Score: 105
Period size: 30 Copynumber: 2.6 Consensus size: 31
4214 CTTAATAATC
4224 AACCGCGCACACTTAGTGCCATGT-AC-TTTA
1 AACC-CGCACACTTAGTGCCATGTAACATTTA
*
4254 AACTCGCACACTTAGTG-C-TGTAACAATTTA
1 AACCCGCACACTTAGTGCCATGTAAC-ATTTA
4284 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
4304 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 13 0.30
30 23 0.53
31 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (31 bp):
AACCCGCACACTTAGTGCCATGTAACATTTA
Found at i:13993 original size:15 final size:15
Alignment explanation
Indices: 13948--14055 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
13938 CCAATATCTC
13948 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
13963 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
13978 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
13993 GAATTTCCA-ATATTT
1 G-ATACCCATATCTTT
14008 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
14023 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
14038 GATACCCATATCTTT
1 GATACCCATATCTTT
14053 GAT
1 GAT
14056 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 14 0.20
15 41 0.59
16 14 0.20
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:14062 original size:30 final size:30
Alignment explanation
Indices: 13938--14061 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
13928 TTTTATTATG
*
13938 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
13969 CCAATATTTGATACCCATATCTTTGAATTT
1 CCAATATTTGATACCCATATCTTTGACTTT
13999 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
14029 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
14059 CCA
1 CCA
14062 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:18682 original size:15 final size:15
Alignment explanation
Indices: 18637--18744 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
18627 CCAATATCTC
18637 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
18652 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
18667 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
18682 GACTTTCTA-ATATTT
1 GA-TACCCATATCTTT
18697 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
18712 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
18727 GATACCCATATCTTT
1 GATACCCATATCTTT
18742 GAT
1 GAT
18745 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:18751 original size:30 final size:30
Alignment explanation
Indices: 18627--18750 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
18617 TTTTATTATG
*
18627 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
18658 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
18688 CTAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
18718 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
18748 CCA
1 CCA
18751 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:20488 original size:41 final size:39
Alignment explanation
Indices: 20430--20553 Score: 108
Period size: 41 Copynumber: 3.0 Consensus size: 39
20420 TGGGGATAGC
*
20430 GATTCAGGCTTTATGCCTAGCATGCTTTGTGCTGGTGTATT
1 GATTCAGGCTTTGTGCCTAGCA-GCTTTGTGC-GGTGTATT
*
20471 GATTCAGGCTTTGTGCCTAACCAGCTTCATGT-CGGTGTATT
1 GATTCAGGCTTTGTGCCT-AGCAGCTT--TGTGCGGTGTATT
* * * *
20512 G-TATCAGGCCTTGAGCCTAGCAAGCTTCGTGCCAGTGTATT
1 GAT-TCAGGCTTTGTGCCTAGC-AGCTTTGTG-CGGTGTATT
20553 G
1 G
20554 TATCAGGTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
39 2 0.03
40 3 0.04
41 57 0.83
42 4 0.06
43 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (39 bp):
GATTCAGGCTTTGTGCCTAGCAGCTTTGTGCGGTGTATT
Found at i:20554 original size:41 final size:41
Alignment explanation
Indices: 20444--20560 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 41
20434 CAGGCTTTAT
* * * * *
20444 GCCTAGCATGCTTTGTGCTGGTGTATTG-ATTCAGGCTTTGT
1 GCCTAGCAAGCTTCGTGCCGGTGTATTGTA-TCAGGCCTTGA
* * * *
20485 GCCTAACCAGCTTCATGTCGGTGTATTGTATCAGGCCTTGA
1 GCCTAGCAAGCTTCGTGCCGGTGTATTGTATCAGGCCTTGA
*
20526 GCCTAGCAAGCTTCGTGCCAGTGTATTGTATCAGG
1 GCCTAGCAAGCTTCGTGCCGGTGTATTGTATCAGG
20561 TAACTTGTAC
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 60 0.98
42 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.34
Consensus pattern (41 bp):
GCCTAGCAAGCTTCGTGCCGGTGTATTGTATCAGGCCTTGA
Found at i:28662 original size:22 final size:25
Alignment explanation
Indices: 28628--28678 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 25
28618 GATGACATAT
28628 TTAATATATAAAAAAGAAAT-AA-C
1 TTAATATATAAAAAAGAAATGAATC
28651 TTAATA-ATAAAAAAGAAATGAATC
1 TTAATATATAAAAAAGAAATGAATC
28675 TTAA
1 TTAA
28679 AAAAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.50
23 8 0.31
24 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (25 bp):
TTAATATATAAAAAAGAAATGAATC
Found at i:28699 original size:14 final size:16
Alignment explanation
Indices: 28660--28699 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 16
28650 CTTAATAATA
28660 AAAAAGAAATGAATCTT
1 AAAAAGAAAT-AATCTT
28677 AAAAA-AAAT-AT-TT
1 AAAAAGAAATAATCTT
28690 AAAAAGAAAT
1 AAAAAGAAAT
28700 GAAATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
16 4 0.18
17 5 0.23
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (16 bp):
AAAAAGAAATAATCTT
Found at i:28772 original size:13 final size:13
Alignment explanation
Indices: 28754--28780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28744 GACACCTGTT
28754 TCCTCCCAAATGG
1 TCCTCCCAAATGG
28767 TCCTCCCAAATGG
1 TCCTCCCAAATGG
28780 T
1 T
28781 GGAAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (13 bp):
TCCTCCCAAATGG
Found at i:34942 original size:18 final size:18
Alignment explanation
Indices: 34919--34953 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34909 CTCCATTAAA
34919 AGTTTTTATT-TACAATAT
1 AGTTTTT-TTGTACAATAT
34937 AGTTTTTTTGTACAATA
1 AGTTTTTTTGTACAATA
34954 AAAACTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (18 bp):
AGTTTTTTTGTACAATAT
Found at i:36950 original size:29 final size:31
Alignment explanation
Indices: 36918--36980 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
36908 TTTTAGCTGT
* *
36918 ATTTGGCCTTCAACCTATT-AAAAAG-GTT-A
1 ATTTGACCATCAACCT-TTCAAAAAGAGTTGA
36947 ATTTGACCATCAACCTTTCAAAAAGAGTTGA
1 ATTTGACCATCAACCTTTCAAAAAGAGTTGA
36978 ATT
1 ATT
36981 AATTTTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 20 0.69
30 3 0.10
31 4 0.14
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (31 bp):
ATTTGACCATCAACCTTTCAAAAAGAGTTGA
Found at i:37893 original size:29 final size:29
Alignment explanation
Indices: 37851--37909 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
37841 TTATGTAAAA
37851 TTTAAAGTATAAAGATTAAATCTCAAGTC
1 TTTAAAGTATAAAGATTAAATCTCAAGTC
37880 TTTAAAGTATAAAGATTAAATCTCAAGTC
1 TTTAAAGTATAAAGATTAAATCTCAAGTC
37909 T
1 T
37910 AAGTGTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (29 bp):
TTTAAAGTATAAAGATTAAATCTCAAGTC
Found at i:44758 original size:39 final size:40
Alignment explanation
Indices: 44585--44775 Score: 269
Period size: 40 Copynumber: 4.8 Consensus size: 40
44575 GGATATAGCT
* * *
44585 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
44625 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
44665 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
44705 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
44744 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
44776 TTATCATCCA
Statistics
Matches: 138, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 33 0.24
40 103 0.75
41 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Done.