Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2293
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: 13231
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Found at i:6308 original size:50 final size:50
Alignment explanation
Indices: 6238--6574 Score: 383
Period size: 51 Copynumber: 6.7 Consensus size: 50
6228 TATCATTCGA
* *
6238 TACACGTAGTAGCCTTCACATAGTACTACACATGTGATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
* *
6288 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
* *
6338 TTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGG
* * * *** *
6389 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CGG
* * *
6440 TTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGG
* * * * * *
6491 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACC-ATTATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGT-TTTA-CGG
*
6542 TACACGTAGTAGCCTTCACACAGTACTACACAC
1 TACACGTAGTAGCCTTCACATAGTACTACACAC
6575 ATGTTCATCG
Statistics
Matches: 243, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.00
49 6 0.02
50 86 0.35
51 143 0.59
52 5 0.02
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
Found at i:6467 original size:102 final size:102
Alignment explanation
Indices: 6234--6574 Score: 481
Period size: 102 Copynumber: 3.4 Consensus size: 102
6224 CTTTTATCAT
* * * * *
6234 TCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGATC-AAG-TTTTACGGTTCACGTAG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * * ***
6297 TAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
6335 -CGGTTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
6399 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
6436 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
*
6501 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
6538 TCGATACACGTAGTAGCCTTCACACAGTACTACACAC
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACAC
6575 ATGTTCATCG
Statistics
Matches: 217, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
100 37 0.17
101 45 0.21
102 135 0.62
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:7094 original size:29 final size:31
Alignment explanation
Indices: 7046--7103 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
7036 GCTTCGACTC
7046 AACTTTTGTCAAAATTACA-TTTTGTCCCTA
1 AACTTTTGTCAAAATTACATTTTTGTCCCTA
*
7076 AACTTTTG-CATAATTACATTTTTGTCCC
1 AACTTTTGTCAAAATTACATTTTTGTCCC
7104 CAAGCTCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (31 bp):
AACTTTTGTCAAAATTACATTTTTGTCCCTA
Found at i:8246 original size:52 final size:52
Alignment explanation
Indices: 8163--8267 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
8153 TGGTTAAGTC
*
8163 TATCAAAATTTTGTTGGTATTTTTCTTCTTCATGGGCAGCTTTAACCATGGA
1 TATCAAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
*
8215 TATCCAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
1 TATCAAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
8267 T
1 T
8268 GGTCTTTGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (52 bp):
TATCAAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
Found at i:10427 original size:47 final size:47
Alignment explanation
Indices: 10310--10758 Score: 715
Period size: 47 Copynumber: 9.6 Consensus size: 47
10300 CCCTTCGGGA
* * * * * *
10310 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACT-CG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10355 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10403 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10450 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10497 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10544 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10591 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10640 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10687 CTTATCACAT-TATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10733 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
10759 CACAATTATC
Statistics
Matches: 376, Mismatches: 22, Indels: 10
0.92 0.05 0.02
Matches are distributed among these distances:
45 2 0.01
46 79 0.21
47 246 0.65
48 2 0.01
49 47 0.12
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.