Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1020
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: 15270
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:1299 original size:28 final size:26
Alignment explanation
Indices: 1257--1331 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
1247 AAAAGTAGCT
* * *
1257 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
* *
1285 AAATTACTGTTATACCTCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
1311 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
1332 GGTTAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 22 0.55
27 1 0.03
28 17 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:1476 original size:27 final size:27
Alignment explanation
Indices: 1435--1547 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
1425 GAGGAAGCGT
*
1435 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1462 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
1489 TCTGGTGGCTCTGCCACGATTATCTATA
1 TCTGGTGGCTCTGCCACAAATATCT-GA
* * * *
1517 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
1543 TCTGG
1 TCTGG
1548 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:1540 original size:54 final size:54
Alignment explanation
Indices: 1433--1547 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
1423 TGGAGGAAGC
*
1433 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * * *
1487 GTTCTGGTGGCTCTGCCACGATTATCTATATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCT-GATCTGGTGACTCTGCCACATATATCT
1541 GTTCTGG
1 GTTCTGG
1548 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:3905 original size:40 final size:40
Alignment explanation
Indices: 3812--4026 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
3802 CGGATGATAA
* * *
3812 CCGGGCTAAGTCCCGAAGGCATTTGCGC-TGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
3851 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
3891 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
3931 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
3971 CCGGGCTATGTCCCG-AGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
4009 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
4027 TACTTCGCTT
Statistics
Matches: 156, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
37 11 0.07
38 18 0.12
39 32 0.21
40 95 0.61
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:11933 original size:39 final size:40
Alignment explanation
Indices: 11851--12066 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
11841 TGGATGATAA
* * *
11851 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-TAT
11891 CCGGGCTAAGTCCCGAA-GCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
*
11930 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
* *
11969 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
* * * *
12009 CCGAGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTA-CTATAT
* *
12049 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
12067 TACTTGGCTT
Statistics
Matches: 158, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 6 0.04
39 74 0.47
40 78 0.49
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
Found at i:12007 original size:79 final size:80
Alignment explanation
Indices: 11851--12066 Score: 271
Period size: 79 Copynumber: 2.7 Consensus size: 80
11841 TGGATGATAA
* * * *
11851 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAA-GCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTG
11914 GTGCAAGTTACTATAT
65 GTGCAAGTTACTATAT
* *
11930 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
*
11994 TGCGAGTTACTATAT
66 TGCAAGTTACTATAT
* * * * *
12009 CCGAGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
12067 TACTTGGCTT
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
77 1 0.01
78 40 0.33
79 56 0.46
80 24 0.20
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
TGCAAGTTACTATAT
Done.