Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2970
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: 20781
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6041 original size:11 final size:11
Alignment explanation
Indices: 6025--6080 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
6015 ACAGGACTTG
*
6025 TTCGACCATGA
1 TTCGACAATGA
6036 TTCGACAATGA
1 TTCGACAATGA
* * *
6047 TTCAACAGTAA
1 TTCGACAATGA
*
6058 TTTGA-AATGA
1 TTCGACAATGA
*
6068 TTCGACTATGA
1 TTCGACAATGA
6079 TT
1 TT
6081 GGTATTGGAA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
10 7 0.21
11 27 0.79
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (11 bp):
TTCGACAATGA
Found at i:6227 original size:51 final size:48
Alignment explanation
Indices: 6149--6262 Score: 140
Period size: 51 Copynumber: 2.3 Consensus size: 48
6139 AGGGTATTAG
* *
6149 TTGGCTTCGGGCCATGATATTGACACTTCGGGG-TGCGAGTTATGCCTTGAT
1 TTGGCTTCGGGCCATGATATAGACACTTCGGGGAT--AAGTTAT--CTTGAT
* *
6200 TTGGCTTCGGGCCATGGTATAGGCACTTCGGGGATAAGTTATCTTGAT
1 TTGGCTTCGGGCCATGATATAGACACTTCGGGGATAAGTTATCTTGAT
*
6248 TTGGCTACGGGCCAT
1 TTGGCTTCGGGCCAT
6263 AAAATAGGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
48 20 0.35
50 6 0.11
51 30 0.53
52 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (48 bp):
TTGGCTTCGGGCCATGATATAGACACTTCGGGGATAAGTTATCTTGAT
Found at i:11325 original size:37 final size:37
Alignment explanation
Indices: 11275--11433 Score: 191
Period size: 37 Copynumber: 4.2 Consensus size: 37
11265 ATATTCGATG
11275 ATATCCGGCTAAGTCCC-AAGCCTTTTGCTAGTGACT
1 ATATCCGGCTAAGTCCCGAAGCCTTTTGCTAGTGACT
*
11311 ATATCCGGGCTAAGTCCCGAAGGC-TTTGCTAGTGAC-
1 ATATCC-GGCTAAGTCCCGAAGCCTTTTGCTAGTGACT
*
11347 ATATCCGGCTAAGTCCCGAAGGCATTTTGCTAGTGACT
1 ATATCCGGCTAAGTCCCGAA-GCCTTTTGCTAGTGACT
* * *
11385 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCC-GGCTAAGTCCCGAA-GCCTTT-TGCTAG-TGACT
11425 ATATCCGGC
1 ATATCCGGC
11434 AATCCGAAGG
Statistics
Matches: 110, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
35 14 0.13
36 13 0.12
37 35 0.32
38 10 0.09
39 23 0.21
40 13 0.12
41 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (37 bp):
ATATCCGGCTAAGTCCCGAAGCCTTTTGCTAGTGACT
Found at i:11394 original size:74 final size:73
Alignment explanation
Indices: 11275--11413 Score: 235
Period size: 74 Copynumber: 1.9 Consensus size: 73
11265 ATATTCGATG
* *
11275 ATATCCGGCTAAGTCCCAAGCCTTTTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC-TTTG
1 ATATCCGGCTAAGTCCCAAGCATTTTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTG
11339 CTAGTGAC
66 CTAGTGAC
11347 ATATCCGGCTAAGTCCCGAAGGCATTTTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGCTAAGTCCC-AA-GCATTTTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATT
11412 TG
64 TG
11414 TGCGAGTTGC
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 17 0.27
73 2 0.03
74 39 0.63
75 4 0.06
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (73 bp):
ATATCCGGCTAAGTCCCAAGCATTTTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTG
CTAGTGAC
Found at i:14083 original size:50 final size:50
Alignment explanation
Indices: 14003--14143 Score: 196
Period size: 50 Copynumber: 2.8 Consensus size: 50
13993 GGGTAAGGTA
* * * * *
14003 CCGACGCCATGTCCCTGACATAGTCTTACACT-GTTTCTCATCTATCG-GTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATATATCGAG-G
*
14053 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAGG
14103 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT
14144 GTCTCCCTAG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
50 81 0.98
51 2 0.02
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (50 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCGAGG
Found at i:15805 original size:1 final size:1
Alignment explanation
Indices: 15799--15876 Score: 156
Period size: 1 Copynumber: 78.0 Consensus size: 1
15789 CAGGTGTTGT
15799 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
15864 GGGGGGGGGGGGG
1 GGGGGGGGGGGGG
15877 TGTGTCCCTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:17871 original size:42 final size:42
Alignment explanation
Indices: 17712--17872 Score: 189
Period size: 41 Copynumber: 3.8 Consensus size: 42
17702 TACCGTACCA
* * *
17712 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
* * * * * * * *
17754 ATGCTAATAGCCAAGCTGTAGTTTTACACGAAGTCTCATATCG
1 ATGC-CATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
* *
17797 ATGCCATATCCCAGA-ATGGTCTTGCACGTAGTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
17838 ATGCCATATCCCAGATATGGTCTTACACGTAGTCT
1 ATGCCATATCCCAGATATGGTCTTACACGTAGTCT
17873 TAGTAACCCT
Statistics
Matches: 95, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
41 35 0.37
42 29 0.31
43 31 0.33
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
Found at i:18278 original size:1 final size:1
Alignment explanation
Indices: 18272--18341 Score: 140
Period size: 1 Copynumber: 70.0 Consensus size: 1
18262 TTTTCATCCA
18272 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18337 TTTTT
1 TTTTT
18342 CTTCATTATC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19673 original size:14 final size:15
Alignment explanation
Indices: 19651--19685 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
19641 GAAAAATTAT
*
19651 ATTATTAATTAT-AA
1 ATTAATAATTATAAA
19665 ATTAATAATTATAAA
1 ATTAATAATTATAAA
19680 ATTAAT
1 ATTAAT
19686 TCAGAGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAATAATTATAAA
Done.