Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3502
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: 34283
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:3381 original size:27 final size:27
Alignment explanation
Indices: 3351--3555 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
3341 ATATTAAGTC
* *
3351 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
3378 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
3406 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
3433 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
3460 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
3487 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
3514 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
3541 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3556 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:3490 original size:54 final size:54
Alignment explanation
Indices: 3351--3554 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
3341 ATATTAAGTC
* * * **
3351 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
3406 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
3460 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
3514 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
3555 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:3520 original size:81 final size:81
Alignment explanation
Indices: 3405--3554 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
3395 ATAATCAAAC
* * * * * *
3405 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
3470 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
3486 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
3551 GTGC
66 GTGC
3555 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:11478 original size:27 final size:27
Alignment explanation
Indices: 11448--11625 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
11438 ATATTAAGTC
* *
11448 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
11475 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
11503 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
11530 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
11557 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
11584 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
11611 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11626 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.80
28 26 0.20
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:11587 original size:54 final size:54
Alignment explanation
Indices: 11448--11625 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
11438 ATATTAAGTC
* * * **
11448 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
11503 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
11557 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
11611 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11626 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:20573 original size:28 final size:28
Alignment explanation
Indices: 20511--20661 Score: 232
Period size: 28 Copynumber: 5.4 Consensus size: 28
20501 GAGATTGGCG
* * *
20511 CTAAGTGTGCGGGTTTAAATTGTATAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
20540 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20568 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20596 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
20624 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20651 CTGAGTGTGCG
1 CTAAGTGTGCG
20662 GACTTAATAT
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
27 23 0.20
28 78 0.67
29 15 0.13
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:24776 original size:40 final size:40
Alignment explanation
Indices: 24689--24919 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
24679 CATTTGAATG
* * * *
24689 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
*
24728 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * * * *
24768 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
* *
24808 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
24848 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * *
24888 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
24920 TTGTGGTTAT
Statistics
Matches: 166, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 15 0.09
40 147 0.89
41 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
Found at i:24917 original size:120 final size:119
Alignment explanation
Indices: 24689--24939 Score: 407
Period size: 120 Copynumber: 2.1 Consensus size: 119
24679 CATTTGAATG
* * *
24689 ATATCCGGGCTAAGTCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
1 ATATCCGGGCTAAGCCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCAT
24754 TTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
66 TTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
24808 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAG-CCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGC
* *
24872 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
64 ATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
24928 ATATCC-GGCTAA
1 ATATCCGGGCTAA
24940 ATTCCGAAGA
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
119 19 0.16
120 100 0.82
121 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (119 bp):
ATATCCGGGCTAAGCCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:24935 original size:80 final size:80
Alignment explanation
Indices: 24689--24919 Score: 331
Period size: 80 Copynumber: 2.9 Consensus size: 80
24679 CATTTGAATG
* *
24689 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
24753 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGAT
* * *
24768 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
24833 TTTGTGCGAGTTGAT
66 TTTGTGCGAGTTGAT
* * * * *
24848 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTTTATCCGGGCTAAGACCCGAAGGC
*
24912 AATTGTGC
65 ATTTGTGC
24920 TTGTGGTTAT
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 12 0.09
80 121 0.90
81 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGAT
Found at i:32850 original size:39 final size:40
Alignment explanation
Indices: 32712--32940 Score: 295
Period size: 39 Copynumber: 5.8 Consensus size: 40
32702 CATTTGAATG
* * *
32712 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
* *
32752 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * * *
32792 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
32831 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
32871 ATAT-CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * *
32910 ATA-CCCGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
32941 TTGTGGTTAT
Statistics
Matches: 165, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 94 0.57
40 69 0.42
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Done.