Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1702
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: 29123
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8156 original size:40 final size:40
Alignment explanation
Indices: 8101--8331 Score: 340
Period size: 40 Copynumber: 5.8 Consensus size: 40
8091 GGATATAGCT
* * *
8101 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
8141 ACTCACACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
8181 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
8221 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
8261 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
8300 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
8332 TTATCATCCA
Statistics
Matches: 176, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 33 0.19
40 141 0.80
41 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:10718 original size:48 final size:48
Alignment explanation
Indices: 10593--10925 Score: 352
Period size: 48 Copynumber: 6.9 Consensus size: 48
10583 AAAGGTTAAG
* * *
10593 ATGCCGATGCCATGTCCCAGACATGATCTTACACTGGCTCTCATATATCA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATA-A-CA
* * ** *
10643 ATGCCGATGCAATGTCCCTGACATGGTCTTACACTAGCTCTCATAACA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACA
* * * *
10691 ATGCTGAGGCCATATTCCAAACATGGTCTTACACTAGCTCTCATGAA-A
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAT-AACA
* *
10739 ATGCCGAGGCCATGTTCCAAACATGGTCTTACACTGGCTCAT-ACAACA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC-TCATAACA
* * * *
10787 ATGTCGATACTATGTTCCAAACATGGTCTTACACTGGCTCAT-ATAATA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC-TCATAACA
* * *
10835 ATGCCGATGCCATGTTCCAAACATGG--TTACACTAGCTCACATATCA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACA
* * * * *
10881 AAGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATA
10926 TAACCCTAGT
Statistics
Matches: 244, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
46 37 0.15
47 2 0.01
48 160 0.66
49 4 0.02
50 41 0.17
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (48 bp):
ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAACA
Found at i:10855 original size:144 final size:142
Alignment explanation
Indices: 10593--10921 Score: 403
Period size: 144 Copynumber: 2.3 Consensus size: 142
10583 AAAGGTTAAG
* * * *
10593 ATGCCGATGCCATGTCCCAGACATGATCTTACACTGGCTCTCATATATCAATGCCGATGCAATGT
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCATACAACAATGCCGATACAATGT
** *
10658 CCCTGACATGGTCTTACACTAGCTCTCATAACAATGCTGAGGCCATATTCCAAACATGGTCTTAC
64 CCCAAACATGGTCTTACACTAGCTCTCATAACAATGCCGAGGCCATATTCCAAACATGG--TTAC
*
10723 ACTAGCTCTCATGA-AA
127 ACTAGCTCACAT-ACAA
* * * * * *
10739 ATGCCGAGGCCATGTTCCAAACATGGTCTTACACTGGCTCATACAACAATGTCGATACTATGTTC
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACAACAATGCCGATACAATGTCC
* * * *
10804 CAAACATGGTCTTACACTGGCTCAT-ATAATAATGCCGATGCCATGTTCCAAACATGGTTACACT
66 CAAACATGGTCTTACACTAGCTC-TCATAACAATGCCGAGGCCATATTCCAAACATGGTTACACT
10868 AGCTCACATATCAA
130 AGCTCACATA-CAA
*
10882 A-GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCA
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA
10922 CATATAACCC
Statistics
Matches: 158, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
141 1 0.01
142 50 0.32
143 3 0.02
144 70 0.44
145 1 0.01
146 33 0.21
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (142 bp):
ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACAACAATGCCGATACAATGTCC
CAAACATGGTCTTACACTAGCTCTCATAACAATGCCGAGGCCATATTCCAAACATGGTTACACTA
GCTCACATACAA
Found at i:13800 original size:26 final size:27
Alignment explanation
Indices: 13758--13825 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
13748 ACACACCTTA
* *
13758 GCTCTT-ATGAACATCCCGATATA-TG
1 GCTCTTCATGAACTTCCCGATAAATTG
* *
13783 GCTCTTCATGAGCTTCCCGTTAAATTG
1 GCTCTTCATGAACTTCCCGATAAATTG
* *
13810 GCTCTTCGTGACCTTC
1 GCTCTTCATGAACTTC
13826 GTGATAGTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 6 0.17
26 13 0.37
27 16 0.46
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (27 bp):
GCTCTTCATGAACTTCCCGATAAATTG
Found at i:14061 original size:24 final size:23
Alignment explanation
Indices: 13990--14068 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
13980 AGCCTGGATA
13990 AGCTTCCCAAAAGGCTCTTTATG
1 AGCTTCCCAAAAGGCTCTTTATG
14013 AGCTTCCCAAAAGGCTCTTTATG
1 AGCTTCCCAAAAGGCTCTTTATG
* * * *
14036 AGTTTCCTAAAATGGCTCTGTGTG
1 AGCTTCCCAAAA-GGCTCTTTATG
14060 AGCTTCCCA
1 AGCTTCCCA
14069 TTATAAGACT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
23 33 0.67
24 16 0.33
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (23 bp):
AGCTTCCCAAAAGGCTCTTTATG
Found at i:16906 original size:45 final size:44
Alignment explanation
Indices: 16821--16906 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
16811 TATGTAATTT
* * *
16821 GAACTCATTGAGTTGTGTTTGAGTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTGGGTCTGAGTTCATGATATATATGACATCC
* *
16865 GAACTCATTGAGTTGGGGTCTGAGTTCGTGATATGTATGACA
1 GAACTCATTGAGTT-GGGTCTGAGTTCATGATATATATGACA
16907 CATGTTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 14 0.39
45 22 0.61
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (44 bp):
GAACTCATTGAGTTGGGTCTGAGTTCATGATATATATGACATCC
Found at i:20990 original size:16 final size:16
Alignment explanation
Indices: 20971--21001 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20961 CTTATTCACT
20971 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
20987 TACTTACTTACTTAA
1 TACTCACTTACTTAA
21002 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:21007 original size:20 final size:20
Alignment explanation
Indices: 20968--21007 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20958 AAACTTATTC
* *
20968 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
20988 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
21008 TTATTAATAA
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:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:21376 original size:55 final size:53
Alignment explanation
Indices: 21241--21448 Score: 187
Period size: 55 Copynumber: 3.8 Consensus size: 53
21231 ATCCTTTTGA
* * *
21241 AACTTACCATTGCCATGTCTCGACATGGTCTTACATG-GTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGTG-ATCCTTG-CTTATAG
*
21294 AACTCACCAATGCCATGCCTT-AGCATGGTCTTACATGTGA-CCTTTGCGTTATAG
1 AACTTACCAATGCCATGCCTTGA-CATGGTCTTACATGTGATCC-TTGC-TTATAG
* * * *
21348 TAACTTATCAATGCCATGTCTTGACATGGCCTTACATGAT-ATCCTTGCCT-TAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATG-TGATCCTTGCTTATAG
*
21401 AAACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATG-GTATCCTT
1 -AA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGTG-ATCCTT
21449 AAACCCTAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 24
0.77 0.08 0.14
Matches are distributed among these distances:
52 4 0.03
53 44 0.34
54 10 0.08
55 66 0.52
56 4 0.03
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGTGATCCTTGCTTATAG
Found at i:21385 original size:108 final size:110
Alignment explanation
Indices: 21241--21440 Score: 307
Period size: 108 Copynumber: 1.8 Consensus size: 110
21231 ATCCTTTTGA
* * *
21241 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGCCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
21304 -TGCCATGCCTTAGCATGGTCTTACATGTGACCTTTGCGTTATAGT
65 TTGCCATGCCTTAGCATGGTCTTACATGTGACCTTTGCGTTATAGT
* * *
21349 AACTTATCAATGCCATGTCTTGACATGGCCTTACATGATATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGCCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
21414 TGCCATGCCTTGGCATGGTCTTACATG
66 TGCCATGCCTTAGCATGGTCTTACATG
21441 GTATCCTTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 26 0.32
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGCCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTAGCATGGTCTTACATGTGACCTTTGCGTTATAGT
Found at i:23993 original size:15 final size:15
Alignment explanation
Indices: 23973--24003 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23963 TAGAAATTCG
23973 ACCAATTTTAAGTTC
1 ACCAATTTTAAGTTC
23988 ACCAATTTTAAGTTC
1 ACCAATTTTAAGTTC
24003 A
1 A
24004 TGGACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (15 bp):
ACCAATTTTAAGTTC
Done.