Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold879
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: 8640
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1340 original size:51 final size:50
Alignment explanation
Indices: 1171--1488 Score: 325
Period size: 48 Copynumber: 6.5 Consensus size: 50
1161 CAGCAGCCGC
* * * * *
1171 AAACGCAGACGCTGTTTATGCAACAATCAC--CGCTTCCGCCTCCAAAAG
1 AAACGCAAACGCTATTTATGCAACAACCACGGCGCCTCCGCCTCCGAAAG
* * *
1219 AAACGCAAACTCTATTTATGCAACCA-C-CGGCACCTCCGCCTCCGAAAAG
1 AAACGCAAACGCTATTTATGCAACAACCACGGCGCCTCCGCCTCCG-AAAG
* * * * *
1268 AGACGCAGACGCTGTTTATGCAACAACCACAGGCGCCTCCGCCTCCCAAGG
1 AAACGCAAACGCTATTTATGCAACAACCAC-GGCGCCTCCGCCTCCGAAAG
*
1319 AAACGCAAACGCTATTTATGCAACAACTGC-CGGCGCCTCCACCTCCGAAAG
1 AAACGCAAACGCTATTTATGCAACAAC--CACGGCGCCTCCGCCTCCGAAAG
* * *
1370 AAACGCAGACGCTATTTATG---CAACCATCGGCGCCTCCACCTCCGAAGG
1 AAACGCAAACGCTATTTATGCAACAACCA-CGGCGCCTCCGCCTCCGAAAG
* *
1418 AAACGCAAACGCTATTTATGCAAC--CGC-CGGCCCCTCCTCCTCCGAAAG
1 AAACGCAAACGCTATTTATGCAACAAC-CACGGCGCCTCCGCCTCCGAAAG
*
1466 AAACGCAAACGCTGTTTATGCAA
1 AAACGCAAACGCTATTTATGCAA
1489 ACGCCACATA
Statistics
Matches: 228, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
46 2 0.01
47 1 0.00
48 116 0.51
49 26 0.11
50 2 0.01
51 65 0.29
52 15 0.07
53 1 0.00
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.17
Consensus pattern (50 bp):
AAACGCAAACGCTATTTATGCAACAACCACGGCGCCTCCGCCTCCGAAAG
Found at i:1768 original size:33 final size:33
Alignment explanation
Indices: 1718--1831 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 33
1708 TCAGTTGGTT
*
1718 CGAGCCAGATTAGTCGGCCCGAGCCTACACGGA
1 CGAGCCAGATTAATCGGCCCGAGCCTACACGGA
* *
1751 CGAGCCAGCTTAATCGGCCGGAGCCTACACAGG-
1 CGAGCCAGATTAATCGGCCCGAGCCTACAC-GGA
* * *
1784 CGAGCCAGGTTAATCGGCCTGAGCCCTTC-CGGA
1 CGAGCCAGATTAATCGGCCCGAG-CCTACACGGA
*
1817 CGAGCCCGATTAATC
1 CGAGCCAGATTAATC
1832 AGATAGGAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.03
33 62 0.89
34 6 0.09
ACGTcount: A:0.23, C:0.33, G:0.29, T:0.15
Consensus pattern (33 bp):
CGAGCCAGATTAATCGGCCCGAGCCTACACGGA
Found at i:1912 original size:3 final size:3
Alignment explanation
Indices: 1904--1932 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1894 AATCAGACAG
1904 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1933 ACTACTACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:8064 original size:11 final size:11
Alignment explanation
Indices: 8048--8073 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8038 AGGATAGCAA
8048 AAAATAAAAAT
1 AAAATAAAAAT
8059 AAAATAAAAAT
1 AAAATAAAAAT
8070 AAAA
1 AAAA
8074 AATCACTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:8463 original size:11 final size:11
Alignment explanation
Indices: 8425--8522 Score: 55
Period size: 11 Copynumber: 9.0 Consensus size: 11
8415 TAAAAATTTA
8425 TTTTATATT-T
1 TTTTATATTAT
*
8435 TTGATATATTCAT
1 TT-TTATATT-AT
8448 ATTTTATATTAT
1 -TTTTATATTAT
*
8460 TTTTAT-TAAT
1 TTTTATATTAT
*
8470 TTTTAAATTA-
1 TTTTATATTAT
* *
8480 TATCATATT-T
1 TTTTATATTAT
8490 TTATT-TATT-T
1 TT-TTATATTAT
8500 TTTTCATATTAT
1 TTTT-ATATTAT
*
8512 GTTTATATTAT
1 TTTTATATTAT
8523 ATTATCGTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
9 2 0.03
10 24 0.36
11 26 0.39
12 6 0.09
13 7 0.10
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:8511 original size:31 final size:29
Alignment explanation
Indices: 8443--8511 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 29
8433 TTTTGATATA
*
8443 TTCATATTTTATATTATTTTTATTAATTT
1 TTCATATTATATATTATTTTTATTAATTT
* *
8472 TT-AAATTATATCA-TATTTTTATTTATTTTT
1 TTCATATTATAT-ATTATTTTTA-TTA-ATTT
8502 TTCATATTAT
1 TTCATATTAT
8512 GTTTATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 15 0.47
29 6 0.19
30 5 0.16
31 6 0.19
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (29 bp):
TTCATATTATATATTATTTTTATTAATTT
Done.