Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold650
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: 60055
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:7792 original size:40 final size:40
Alignment explanation
Indices: 7755--7886 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
7745 GCTACTCGTT
**
7755 CAAATGCCTTCGGGACATAGTCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* *
7795 GAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
7835 CAAATGCCTTCGGG-CTTACCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
7874 CAAATGCCTTCGG
1 CAAATGCCTTCGG
7887 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.41
40 46 0.56
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:7874 original size:39 final size:40
Alignment explanation
Indices: 7783--7886 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 40
7773 AGTCCGGTTA
* * *
7783 TAGTAACTCGCAGAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
*
7823 TAGTAACTCGCACAAATGCCTTCGGG-CTTACCCCAGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
*
7862 TAGTATCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
7887 ATCTTAGTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 34 0.58
40 25 0.42
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
Found at i:7899 original size:79 final size:80
Alignment explanation
Indices: 7783--7932 Score: 189
Period size: 79 Copynumber: 1.9 Consensus size: 80
7773 AGTCCGGTTA
* * *
7783 TAGTAACTCGCAGAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCACAAA-GCCTTCG
7847 GG-CTTACCCCAGAAT
65 GGACTTACCCCAGAAT
* ** * *
7862 TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCG
7926 GGACTTA
65 GGACTTA
7933 GCCCGGACAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.05
79 45 0.75
80 12 0.20
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGG
GACTTACCCCAGAAT
Found at i:11046 original size:33 final size:33
Alignment explanation
Indices: 11004--11071 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
10994 GGAACAGATG
11004 TTAGATCAATTGCAGGTAATGAATTCTATTATT
1 TTAGATCAATTGCAGGTAATGAATTCTATTATT
11037 TTAGATCAATTGCAGGTAATGAATTCTATTATT
1 TTAGATCAATTGCAGGTAATGAATTCTATTATT
11070 TT
1 TT
11072 TTAGATGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (33 bp):
TTAGATCAATTGCAGGTAATGAATTCTATTATT
Found at i:29737 original size:13 final size:13
Alignment explanation
Indices: 29719--29745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29709 TATTTTAATC
29719 AGTTAATTAGTTT
1 AGTTAATTAGTTT
29732 AGTTAATTAGTTT
1 AGTTAATTAGTTT
29745 A
1 A
29746 ATAAACAACT
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:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
AGTTAATTAGTTT
Found at i:33032 original size:50 final size:50
Alignment explanation
Indices: 32973--33204 Score: 239
Period size: 50 Copynumber: 4.7 Consensus size: 50
32963 GGGATAAATA
32973 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATG
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATG
* *
33023 AGAGCTAGTGTAAGGCCATGTCTGGGACATGGCATCGG-CT--TGATAT-
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATG
* * * *
33069 -GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATAGATG
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGATATG
* * * * * *
33118 AGAGCCAATGTAAGACCATGT-TAGGGATATGGCTTCGGCCTCGACATACG
1 AGAGCTAGTGTAAGACCATGTCT-GGGACATGGCATCGGCCTCGAGATATG
* *
33168 AG-GGTCAGTGTAAGAGCATG-CATGGGACATGGCATCG
1 AGAGCT-AGTGTAAGACCATGTC-TGGGACATGGCATCG
33205 ACTTTGATGT
Statistics
Matches: 150, Mismatches: 21, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
45 34 0.23
47 6 0.04
48 3 0.02
49 5 0.03
50 101 0.67
51 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (50 bp):
AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATG
Found at i:33087 original size:45 final size:47
Alignment explanation
Indices: 32973--33237 Score: 207
Period size: 50 Copynumber: 5.5 Consensus size: 47
32963 GGGATAAATA
*
32973 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATAT
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTC-AGATAT
* * *
33022 GAGAGCTAGTGTAAGGCCATGTCTGGGACATGGCATCGGCT-TGATAT
1 -AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCAGATAT
* * *
33069 -GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATAGAT
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCAGAT--AT
* * * *
33117 GAGAGCCAATGTAAGACCATGT-TAGGGATATGGCTTCGGCCTC-GACAT
1 -AGAGCCAGTGTAAGACCATGTCT-GGGACATGGCATCGG-CTCAGATAT
* * * ** *
33165 ACGAGGGTCAGTGTAAGAGCATG-CATGGGACATGGCATCGACTTTGATGT
1 A-GA--GCCAGTGTAAGACCATGTC-TGGGACATGGCATCGGCTCAGATAT
* *
33215 GTGAGCCAGTATAAGACCATGTC
1 -AGAGCCAGTGTAAGACCATGTC
33238 CAGGATATGG
Statistics
Matches: 174, Mismatches: 26, Indels: 31
0.75 0.11 0.13
Matches are distributed among these distances:
45 35 0.20
46 3 0.02
47 6 0.03
48 20 0.11
49 6 0.03
50 101 0.58
51 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (47 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCAGATAT
Found at i:33150 original size:95 final size:95
Alignment explanation
Indices: 32979--33156 Score: 261
Period size: 95 Copynumber: 1.9 Consensus size: 95
32969 AATAAGAGCT
* * * *
32979 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGAGCTAGTGTAAGGCCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGATGAGAGCCAATGTAAGACCATGT
33044 CTGGGACATGGCATCGGCTTGATATGTGCC
66 CTGGGACATGGCATCGGCTTGATATGTGCC
*
33074 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATAGATGAGAGCCAATGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGAGATGAGAGCCAATGTAAGACCATG
* *
33138 T-TAGGGATATGGCTTCGGC
65 TCT-GGGACATGGCATCGGC
33157 CTCGACATAC
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
94 1 0.01
95 72 0.97
96 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGATGAGAGCCAATGTAAGACCATGT
CTGGGACATGGCATCGGCTTGATATGTGCC
Found at i:50774 original size:29 final size:29
Alignment explanation
Indices: 50739--50812 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
50729 GTTGTGAGAT
* *
50739 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
50768 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
50797 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
50813 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:59128 original size:29 final size:29
Alignment explanation
Indices: 59093--59166 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
59083 GTTGTGAGAT
* *
59093 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
59122 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
59151 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
59167 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Done.