Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3681
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: 31259
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2683 original size:40 final size:40
Alignment explanation
Indices: 2590--2747 Score: 309
Period size: 40 Copynumber: 4.0 Consensus size: 40
2580 CGGATGATAA
2590 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
2629 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
2669 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
2709 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
2748 AGTCCGAAGG
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
39 38 0.32
40 80 0.68
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:10731 original size:40 final size:40
Alignment explanation
Indices: 10676--10852 Score: 304
Period size: 40 Copynumber: 4.5 Consensus size: 40
10666 CGGATGATAA
10676 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
10716 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
10756 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
10796 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
10836 CC-GGATAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
10853 TACTTGGGTT
Statistics
Matches: 133, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 15 0.11
40 118 0.89
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:18803 original size:40 final size:40
Alignment explanation
Indices: 18748--18964 Score: 357
Period size: 40 Copynumber: 5.5 Consensus size: 40
18738 CGGATGATAA
*
18748 CCGGGCTAAGTCCCGATGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
18788 CCGGGCTAAGTCCCGAAGGTATTTGTGCGAGTTACGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
18828 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18868 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
18908 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
18948 CC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
18965 TTACTTGGGT
Statistics
Matches: 169, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 16 0.09
40 153 0.91
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:21882 original size:27 final size:26
Alignment explanation
Indices: 21826--21882 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
21816 CAACCTTAAC
* *
21826 CCTAGGGGTATAACAGAAATTTTGCT
1 CCTAGGGGTATAACAGAAATTTTCCA
*
21852 CCTAGGGGTA-AATCTGTAAATTTTCCA
1 CCTAGGGGTATAA-CAG-AAATTTTCCA
21879 CCTA
1 CCTA
21883 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.08
26 12 0.46
27 12 0.46
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (26 bp):
CCTAGGGGTATAACAGAAATTTTCCA
Found at i:23139 original size:12 final size:11
Alignment explanation
Indices: 23085--23144 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 11
23075 GGCTAAGGAG
23085 GAAAAGAAGAA
1 GAAAAGAAGAA
* *
23096 GAGAAAGTAGAT
1 GA-AAAGAAGAA
* *
23108 GGAGAGAA-AA
1 GAAAAGAAGAA
23118 GAAAAG-AGAA
1 GAAAAGAAGAA
23128 GAAGAAGAAGAA
1 GAA-AAGAAGAA
23140 GAAAA
1 GAAAA
23145 AACTGAATCC
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
9 1 0.03
10 10 0.27
11 11 0.30
12 15 0.41
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (11 bp):
GAAAAGAAGAA
Found at i:24073 original size:15 final size:15
Alignment explanation
Indices: 24036--24064 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24026 TTTTCCTATC
24036 TAATAATAATAATTA
1 TAATAATAATAATTA
24051 TAATAATAATAATT
1 TAATAATAATAATT
24065 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:24106 original size:25 final size:26
Alignment explanation
Indices: 24051--24112 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
24041 ATAATAATTA
*
24051 TAATAATAATAATTTTATAAATATATC
1 TAATAATAA-AAATTTATAAATATATC
* * *
24078 TAATCATAAAAATTTA-AAATATCTG
1 TAATAATAAAAATTTATAAATATATC
24103 TAATAATAAA
1 TAATAATAAA
24113 TACAGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 16 0.53
26 6 0.20
27 8 0.27
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (26 bp):
TAATAATAAAAATTTATAAATATATC
Found at i:24884 original size:30 final size:30
Alignment explanation
Indices: 24849--24912 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
24839 CAACTTTTAT
*
24849 AATTCTGATAACAATACTGTAGTACTTTTG
1 AATTCTGATAACAATACTGTAGTACTTTCG
** *
24879 AATTCTGATAACGGTATTGTAGTACTTTCG
1 AATTCTGATAACAATACTGTAGTACTTTCG
24909 AATT
1 AATT
24913 TCTGTCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (30 bp):
AATTCTGATAACAATACTGTAGTACTTTCG
Found at i:26938 original size:42 final size:43
Alignment explanation
Indices: 26856--26949 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 43
26846 TCCCAGATGT
** * *
26856 GGTCTTACATGTTATCAAATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACATGAAATCAAATATCGATGCCAATATCCCAGACAG
* *
26899 GGTCTTACATGAAATCATATAT-GATGCCAATATCCCAGACAT
1 GGTCTTACATGAAATCAAATATCGATGCCAATATCCCAGACAG
26941 GGTCTTACA
1 GGTCTTACA
26950 CATCAATCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
42 26 0.58
43 19 0.42
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (43 bp):
GGTCTTACATGAAATCAAATATCGATGCCAATATCCCAGACAG
Found at i:26993 original size:43 final size:44
Alignment explanation
Indices: 26837--26993 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 44
26827 AGCTCGTACA
** **
26837 ATGCCAACGTCCCAGATGTGGTCTT--ACATGTTATCA-AATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACATGAAATCACAA-AT-G
* * *
26880 ATGCC-ACTGTCCCAGACAGGGTCTT--ACATGAAATCATATATG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACATGAAATCACAAATG
** *
26922 ATGCCAATATCCCAGACATGGTCTTACACAT-CAATCACAAATG
1 ATGCCAACGTCCCAGACATGGTCTTACACATGAAATCACAAATG
*
26965 ATGCTAACGTCCCAGACATGGTCTTACAC
1 ATGCCAACGTCCCAGACATGGTCTTACAC
26994 GATAACACAC
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 23 0.24
43 66 0.70
44 5 0.05
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATGAAATCACAAATG
Done.