Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2615
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: 20692
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Found at i:60 original size:29 final size:27
Alignment explanation
Indices: 1--68 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
* *
1 CACTTAGTGCCCGTACTTTAAACTCGCA
1 CACTTAGTG-CCGTACTTTAAACCCGAA
*
29 CACTTAGTGCTGTACAATTTAAACCCGAA
1 CACTTAGTGCCGTAC--TTTAAACCCGAA
58 CACTTAGTGCC
1 CACTTAGTGCC
69 AATCTCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.15
28 9 0.26
29 20 0.59
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCCGTACTTTAAACCCGAA
Found at i:1927 original size:119 final size:118
Alignment explanation
Indices: 1717--1945 Score: 354
Period size: 119 Copynumber: 1.9 Consensus size: 118
1707 ATTTGAATGA
*
1717 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTATCCGGCTAAGACCCGAAGGCATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTATCCGGCTAAGACCCGAAGGCATTT
*
1782 GTGCGAGTTGCTATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATTT
66 GTGCGAGTTGATATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATTT
*
1835 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGA-TTTATCC-GGCTAAGACCCGAAGGCAT
* * * *
1899 TTGTGCGAGTTGATATA-TCTGGTCTAAGACCCGAAGGCATTTGTGCT
64 TTGTGCGAGTTGATATACCCGGGT-TAAGACCCAAAGGCAATTGTGCT
1946 TATGGTTATA
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
118 39 0.39
119 54 0.53
120 8 0.08
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (118 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTATCCGGCTAAGACCCGAAGGCATTT
GTGCGAGTTGATATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATTT
Found at i:1956 original size:40 final size:40
Alignment explanation
Indices: 1716--1964 Score: 255
Period size: 40 Copynumber: 6.3 Consensus size: 40
1706 CATTTGAATG
* *
1716 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGTCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * *
1756 -TATCCGG-CTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGTCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
* *
1794 ATACCCGGGT-TAAGACCCAAAGGCAATTGTGCTAGTGATT
1 ATATCC-GGTCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
1834 TTATCCGGGT-TAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCC-GGTCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
1874 TTATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGTCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
* * *
1913 ATATCTGGTCTAAGACCCGAAGGCATTTGTGCTTA-TGGTT
1 ATATCCGGTCTAAGACCCGAAGGCAATTGTGC-TAGTGATT
1953 ATATCCGG-CTAA
1 ATATCCGGTCTAA
1965 ATTTCGAAGA
Statistics
Matches: 178, Mismatches: 21, Indels: 21
0.81 0.10 0.10
Matches are distributed among these distances:
38 24 0.13
39 53 0.30
40 100 0.56
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGTCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:1958 original size:79 final size:78
Alignment explanation
Indices: 1716--1964 Score: 290
Period size: 79 Copynumber: 3.2 Consensus size: 78
1706 CATTTGAATG
*
1716 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTATCCGG-CTAAGACCCGAAGGCAT
1 ATATCCGGGCTAAG-ACCGAAGGCAATTGTGCTAGTGATTTATCCGGTCTAAGACCCGAAGGCAT
* * *
1780 TTGTGCGAGTTGCT
65 TTGTGCTAGTGGTT
* * *
1794 ATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATTTTATCCGGGT-TAAGACCCGAAGGC
1 ATATCCGGGCTAAGA-CCGAAGGCAATTGTGCTAGTGA-TTTATCC-GGTCTAAGACCCGAAGGC
* *
1858 AATTGTGCTAGTGATT
63 ATTTGTGCTAGTGGTT
* * * * *
1874 TTATCCGGGCTAAGACCGAAGGCATTTGTGCGAGTTGATATATCTGGTCTAAGACCCGAAGGCAT
1 ATATCCGGGCTAAGACCGAAGGCAATTGTGCTAG-TGATTTATCCGGTCTAAGACCCGAAGGCAT
1939 TTGTGCTTA-TGGTT
65 TTGTGC-TAGTGGTT
1953 ATATCC-GGCTAA
1 ATATCCGGGCTAA
1965 ATTTCGAAGA
Statistics
Matches: 144, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
78 42 0.29
79 58 0.40
80 44 0.31
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (78 bp):
ATATCCGGGCTAAGACCGAAGGCAATTGTGCTAGTGATTTATCCGGTCTAAGACCCGAAGGCATT
TGTGCTAGTGGTT
Found at i:16238 original size:28 final size:29
Alignment explanation
Indices: 16198--16269 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
16188 CTCTTCACCG
*
16198 CGCACACTTAGTGCCTGTAC-TTTAAACT
1 CGCACACTTAGTGCCTGTACATTTAAACC
16226 CGCACACTTAGTG-CTGTACAATTTAAACC
1 CGCACACTTAGTGCCTGTAC-ATTTAAACC
*
16255 CGAACACTTAGTGCC
1 CGCACACTTAGTGCC
16270 AATCTCATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 6 0.15
28 13 0.33
29 19 0.49
30 1 0.03
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCTGTACATTTAAACC
Found at i:17970 original size:40 final size:40
Alignment explanation
Indices: 17912--18142 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
17902 ATTTGAATGA
*
17912 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
* * * *
17952 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTT
* * *
17992 TACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
*
18032 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
* * *
18072 TATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTT
* * *
18111 TATCTGGTCTAAGACCCGAAGGCATTTGTGCT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCT
18143 TATGGTTATA
Statistics
Matches: 166, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 32 0.19
40 132 0.80
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
Found at i:18157 original size:119 final size:120
Alignment explanation
Indices: 17911--18161 Score: 375
Period size: 119 Copynumber: 2.1 Consensus size: 120
17901 CATTTGAATG
*
17911 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
17976 TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATT
66 TTTGTGCGAGTTGATATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATT
* *
18031 TTATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
* * * * *
18095 TTTGTGCGAGTTGATATA-TCTGGTCTAAGACCCGAAGGCATTTGTGCTTA-TGGTT
66 TTTGTGCGAGTTGATATACCCGGGT-TAAGACCCAAAGGCAATTGTGC-TAGTGATT
18150 ATATCC-GGCTAA
1 ATATCCGGGCTAA
18162 ATTTCGAAGA
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
118 9 0.08
119 55 0.47
120 54 0.46
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGATATACCCGGGTTAAGACCCAAAGGCAATTGTGCTAGTGATT
Done.