Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2623
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: 22512
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:122 original size:28 final size:28
Alignment explanation
Indices: 59--156 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
49 ATATTAAGTC
*
59 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
86 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
114 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
143 CGCACACTTAGTGC
1 CGCACACTTAGTGC
157 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:4650 original size:47 final size:49
Alignment explanation
Indices: 4599--4718 Score: 126
Period size: 47 Copynumber: 2.5 Consensus size: 49
4589 GAATTGGCGG
*
4599 TTAAGGATACCATGTAAGACCATGTCAAGACATGGCA-TCG-AC-ATTGA
1 TTAAGGATACCATGTAAGACCATGTCAAGACATGGCATTCGCACTA-AGA
* **
4646 TTAAGGACT-CCATGTAAGACCACAG-CAAGATGTGGCATTCGCACTAAGA
1 TTAAGGA-TACCATGTAAGACCA-TGTCAAGACATGGCATTCGCACTAAGA
*
4695 -CAAGGATACCATGTAAGACCATGT
1 TTAAGGATACCATGTAAGACCATGT
4719 TTGAAACATG
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
47 32 0.53
48 23 0.38
49 4 0.07
50 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (49 bp):
TTAAGGATACCATGTAAGACCATGTCAAGACATGGCATTCGCACTAAGA
Found at i:4751 original size:47 final size:47
Alignment explanation
Indices: 4691--4811 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
4681 CATTCGCACT
4691 AAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGGA
1 AAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGGA
* * * *
4738 AAGACAATGATACCATGTAAGACTATGTTTGGAACATGGCATTTGGT
1 AAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGGA
* *
4785 AAGACAAGGATATCATGCAAGACCATG
1 AAGACAAGGATACCATGTAAGACCATG
4812 CCAAGGCATG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (47 bp):
AAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGGA
Found at i:4972 original size:53 final size:54
Alignment explanation
Indices: 4784--5094 Score: 362
Period size: 55 Copynumber: 5.8 Consensus size: 54
4774 TGGCATTTGG
* * * * *
4784 TAAGACAAGGATATCATGCAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTA
* * * * *
4838 TAAGGTAAGGAAATCATGTAAGACCATGTCAAAACATGGCATTGATGAGTTACTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTA
* * * *
4893 TAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAATTC-A
1 TAAGGC-AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTA
*
4946 TAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTA
* * *
5001 TAAGGCAA-AAGTCCCATGTAAGACCATGCCAAGGCATGGCATT-AGTGAGTTC-A
1 TAAGGCAAGGA-TACCATGTAAGACCATGCCAAGACATGGCATTGA-TGAGTTCTA
* *
5054 TAAGGCAAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCA
5095 ATGGTAAGTT
Statistics
Matches: 218, Mismatches: 31, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
52 4 0.02
53 77 0.35
54 49 0.22
55 84 0.39
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTA
Found at i:4993 original size:108 final size:108
Alignment explanation
Indices: 4798--5094 Score: 479
Period size: 108 Copynumber: 2.7 Consensus size: 108
4788 ACAAGGATAT
* * * * *
4798 CATGCAAGACCATGCCAAGGCATGGCATTGAT-AAGTTCTATAAGGTAAGGAAATCATGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAA-TTC-ATAAGGCAAGGATACCATGTAAGAC
* *
4862 CATGTCAAAACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
64 CATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAAGTCC
4907 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAATTCATAAGGCAAGGATACCATGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAATTCATAAGGCAAGGATACCATGTAAGACCA
4972 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAAGTCC
66 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAAGTCC
* * *
5015 CATGTAAGACCATGCCAAGGCATGGCATTAGTGAGTTCATAAGGCAAGGATACCACGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAATTCATAAGGCAAGGATACCATGTAAGACCA
5080 TGTCAAGACATGGCA
66 TGTCAAGACATGGCA
5095 ATGGTAAGTT
Statistics
Matches: 177, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
108 142 0.80
109 33 0.19
110 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (108 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGGTGAATTCATAAGGCAAGGATACCATGTAAGACCA
TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAAGTCC
Found at i:5106 original size:53 final size:54
Alignment explanation
Indices: 4784--5105 Score: 341
Period size: 53 Copynumber: 6.0 Consensus size: 54
4774 TGGCATTTGG
* * * *
4784 TAAGACAAGGATATCATGCAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTA
* * * * * *
4838 TAAGGTAAGGAAATCATGTAAGACCATGTCAAAACATGGCATTGATGAGTTACTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTA
* * *
4893 TAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAA-TTC-A
1 TAAGGC-AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGAT-AAGTTCTA
* *
4946 TAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTA
* * * *
5001 TAAGGCAA-AAGTCCCATGTAAGACCATGCCAAGGCATGGCATT-AGTGAGTTC-A
1 TAAGGCAAGGA-TACCATGTAAGACCATGCCAAGACATGGCATTGA-TAAGTTCTA
* * * *
5054 TAAGGCAAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC
5106 AAAAAGGAAA
Statistics
Matches: 223, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
52 5 0.02
53 82 0.37
54 49 0.22
55 82 0.37
56 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTA
Found at i:9408 original size:32 final size:31
Alignment explanation
Indices: 9334--9408 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 31
9324 CACACACCCA
* * * *
9334 TGTGGCTCACACAACCTAAATGGCCAGCCCG
1 TGTGCCTCACACAACCCAAATGCCCAGACCG
* *
9365 TGTGCCCCACACTACCCAAATAGCCCAGACCG
1 TGTGCCTCACACAACCCAAAT-GCCCAGACCG
*
9397 TGTGTCTCACAC
1 TGTGCCTCACAC
9409 GGTCCAACAC
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.25, C:0.39, G:0.19, T:0.17
Consensus pattern (31 bp):
TGTGCCTCACACAACCCAAATGCCCAGACCG
Found at i:9432 original size:29 final size:29
Alignment explanation
Indices: 9395--9496 Score: 109
Period size: 29 Copynumber: 3.5 Consensus size: 29
9385 TAGCCCAGAC
*
9395 CGTGTGTCTCACACGGTCCAACACACAG-T
1 CGTGTGTCTCACACGATCCAACACA-AGCT
* * *
9424 CGTGTGTCTCACATGATCCAACATATGCT
1 CGTGTGTCTCACACGATCCAACACAAGCT
*
9453 CGTGTGTCTCACACGATCCAGCACAAGGC-
1 CGTGTGTCTCACACGATCCAACACAA-GCT
* *
9482 CATGTGTCACACACG
1 CGTGTGTCTCACACG
9497 GCCTACCACA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
28 1 0.02
29 58 0.95
30 2 0.03
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (29 bp):
CGTGTGTCTCACACGATCCAACACAAGCT
Found at i:14908 original size:13 final size:13
Alignment explanation
Indices: 14870--14913 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
14860 TGATATTCTT
*
14870 TTTATTATTTTAA
1 TTTATTAATTTAA
14883 -TT-TTAATTTTAA
1 TTTATTAA-TTTAA
14895 TTTATTAATTTAA
1 TTTATTAATTTAA
14908 TTTATT
1 TTTATT
14914 TTCTTTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 3 0.11
12 7 0.26
13 13 0.48
14 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTAATTTAA
Found at i:18458 original size:33 final size:33
Alignment explanation
Indices: 18420--18486 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
18410 AGAGGTTCGG
18420 ATGATATCTTAAATGAATTTCAATACGAAATGA
1 ATGATATCTTAAATGAATTTCAATACGAAATGA
* **
18453 ATGATATTTTAAATGAATTTTGATACGAAATGA
1 ATGATATCTTAAATGAATTTCAATACGAAATGA
18486 A
1 A
18487 CTTGATATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGATATCTTAAATGAATTTCAATACGAAATGA
Done.