Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold576
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: 31205
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Found at i:5280 original size:28 final size:27
Alignment explanation
Indices: 5213--5282 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
5203 GGAATATGAT
* *
5213 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTAACCATGCA
* *
5240 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TAACCATGCA
*
5268 GCACTAAGGGTGCGA
1 GCACTAAGTGTGCGA
5283 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAACCATGCA
Found at i:5298 original size:55 final size:53
Alignment explanation
Indices: 5158--5309 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 53
5148 TAAATTGTAC
* * *
5158 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAGGAATATG
1 AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAATATG
* ** * * *
5211 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAA-TATG
* *
5266 TAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGA
5310 GTTGAGTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.48
55 40 0.49
56 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAATATG
Found at i:5314 original size:27 final size:27
Alignment explanation
Indices: 5159--5314 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
5149 AAATTGTACA
* *
5159 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
5186 GCACTAAGTGTGCGAAAGGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
5213 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
5240 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * * *
5268 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
5295 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
5315 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:16712 original size:31 final size:31
Alignment explanation
Indices: 16670--16733 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16660 CCTTTTCATA
*
16670 TTTCATTTTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
16701 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
16732 TT
1 TT
16734 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:16955 original size:25 final size:24
Alignment explanation
Indices: 16947--16999 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 24
16937 GCCTAGCTTC
16947 TTTTAATAACTGGGGCAAAGCCCTT
1 TTTTAATAACTGGGGCAAAG-CCTT
*
16972 TTTTAATAACTGGGGCATAAGCCCT
1 TTTTAATAACTGGGGCA-AAGCCTT
16997 TTT
1 TTT
17000 GCACTTCCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (24 bp):
TTTTAATAACTGGGGCAAAGCCTT
Found at i:17071 original size:9 final size:9
Alignment explanation
Indices: 17057--17113 Score: 60
Period size: 9 Copynumber: 5.9 Consensus size: 9
17047 ATCTCGTGTG
17057 CATATCATA
1 CATATCATA
*
17066 CATATCATGTG
1 CATATCA--TA
17077 CATATCATA
1 CATATCATA
*
17086 CATGTCATGTA
1 CATATCA--TA
17097 CATATCATA
1 CATATCATA
17106 CATATCAT
1 CATATCAT
17114 GTTTATCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 24 0.60
11 16 0.40
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:17076 original size:20 final size:20
Alignment explanation
Indices: 17053--17115 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
17043 GAACATCTCG
17053 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
17073 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
17093 TGTACATATCATACATATCA
1 TGTGCATATCATACATATCA
17113 TGT
1 TGT
17116 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:17098 original size:11 final size:11
Alignment explanation
Indices: 17064--17115 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
17054 GTGCATATCA
17064 TACATATCATG
1 TACATATCATG
*
17075 TGCATATCA--
1 TACATATCATG
*
17084 TACATGTCATG
1 TACATATCATG
17095 TACATATCA--
1 TACATATCATG
17104 TACATATCATG
1 TACATATCATG
17115 T
1 T
17116 TTATCAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 16 0.48
11 17 0.52
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (11 bp):
TACATATCATG
Found at i:22257 original size:40 final size:40
Alignment explanation
Indices: 22196--22447 Score: 271
Period size: 40 Copynumber: 6.3 Consensus size: 40
22186 CATTTGAATG
* * * *
22196 ATATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* *
22236 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * *
22276 ATA-CTCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATC-CGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
*
22316 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* *
22356 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * * ** *
22396 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
22436 ATATCC-GGCTAA
1 ATATCCGGGCTAA
22448 ATTCCGAAGA
Statistics
Matches: 179, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
39 10 0.06
40 163 0.91
41 6 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:22410 original size:120 final size:120
Alignment explanation
Indices: 22196--22447 Score: 391
Period size: 120 Copynumber: 2.1 Consensus size: 120
22186 CATTTGAATG
* * * *
22196 ATATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
*
22261 TTTGTGCGAGTTGCTATACTCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
66 TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * *
22316 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGC
* *
22380 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
65 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
22436 ATATCC-GGCTAA
1 ATATCCGGGCTAA
22448 ATTCCGAAGA
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
119 6 0.05
120 111 0.93
121 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:22440 original size:80 final size:80
Alignment explanation
Indices: 22196--22427 Score: 315
Period size: 80 Copynumber: 2.9 Consensus size: 80
22186 CATTTGAATG
* * * *
22196 ATATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
22261 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGAT
* *
22276 ATA-CTCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGC
1 ATATCT-GGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGC
22340 ATTTGTGCGAGTTGAT
65 ATTTGTGCGAGTTGAT
* * * * *
22356 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTTTATCCGGGCTAAGACCCGAAGGC
*
22420 AATTGTGC
65 ATTTGTGC
22428 TTGTGGTTAT
Statistics
Matches: 134, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
79 1 0.01
80 129 0.96
81 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGAT
Done.