Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2735
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: 50008
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:7818 original size:23 final size:22
Alignment explanation
Indices: 7787--7829 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
7777 CGGCTCAAAA
7787 TACATAATA-TATACATAAATTT
1 TACATAATAGTA-ACATAAATTT
7809 TACATTAATAGTAACATAAAT
1 TACA-TAATAGTAACATAAAT
7830 GTTAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TACATAATAGTAACATAAATTT
Found at i:12647 original size:3 final size:3
Alignment explanation
Indices: 12639--12684 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
12629 TGATGCAAAA
*
12639 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
12685 TGGTAAAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14950 original size:23 final size:22
Alignment explanation
Indices: 14919--14961 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
14909 TGGCTCAAAA
14919 TACATAATA-TATACATAAATTT
1 TACATAATAGTA-ACATAAATTT
14941 TACATTAATAGTAACATAAAT
1 TACA-TAATAGTAACATAAAT
14962 GTTAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TACATAATAGTAACATAAATTT
Found at i:23147 original size:17 final size:17
Alignment explanation
Indices: 23127--23168 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
23117 TTTTTTATTT
*
23127 TTTATTTTTTTCTTTAC
1 TTTATTTTTTACTTTAC
* *
23144 TTTATTTATTACTTTAT
1 TTTATTTTTTACTTTAC
23161 TTTATTTT
1 TTTATTTT
23169 ATTTTACTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTACTTTAC
Found at i:24226 original size:12 final size:12
Alignment explanation
Indices: 24204--24239 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
24194 GTATATTCCT
24204 AAAGTAGAAAAAA
1 AAAG-AGAAAAAA
24217 AAAGAGAAAAAA
1 AAAGAGAAAAAA
24229 AAA-AGAAAAAA
1 AAAGAGAAAAAA
24240 TATAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.35
12 11 0.48
13 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAGAGAAAAAA
Found at i:34818 original size:23 final size:22
Alignment explanation
Indices: 34787--34829 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
34777 CCGCTCAAAA
34787 TACATAATA-TATACATAAATTT
1 TACATAATAGTA-ACATAAATTT
34809 TACATTAATAGTAACATAAAT
1 TACA-TAATAGTAACATAAAT
34830 GTTAACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TACATAATAGTAACATAAATTT
Found at i:39925 original size:27 final size:27
Alignment explanation
Indices: 39895--40072 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39885 ATATTGAGTC
* * * *
39895 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39922 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39949 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39977 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40004 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40031 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40058 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40073 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40034 original size:82 final size:81
Alignment explanation
Indices: 39916--40071 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39906 TGCTATATAA
* *
39916 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39981 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39998 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40062 CACTTAGTGC
65 CACTTAGTGC
40072 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:47958 original size:27 final size:27
Alignment explanation
Indices: 47928--48105 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
47918 ATATTGAGTC
* * * *
47928 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
47955 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
47982 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
48010 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
48037 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
48064 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
48091 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
48106 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:48067 original size:82 final size:81
Alignment explanation
Indices: 47949--48104 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
47939 TGCTATATAA
* *
47949 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
48014 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
48031 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
48095 CACTTAGTGC
65 CACTTAGTGC
48105 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.