Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01785.F1
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: 2043
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Found at i:1405 original size:24 final size:24
Alignment explanation
Indices: 1369--1463 Score: 64
Period size: 24 Copynumber: 3.7 Consensus size: 24
1359 TGAAAGGGAA
* *
1369 AGGAAGGAAGAGGAAGAAGCCAGG
1 AGGAAAGAGGAGGAAGAAGCCAGG
*
1393 AGGAAAGAGGAGGAAGAGGAGGCCAGAA
1 AGGAAAGAGGAGGAAGA--A-GCCAG-G
* * *
1421 AGAAAAGAGAGGAGGAAGAAGCTAAG
1 AG-GAA-AGAGGAGGAAGAAGCCAGG
* *
1447 AGGAAAGCGGAAGAAGA
1 AGGAAAGAGGAGGAAGA
1464 GGCCCAAAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
24 25 0.45
25 2 0.04
26 3 0.05
27 8 0.15
28 3 0.05
29 2 0.04
30 12 0.22
ACGTcount: A:0.49, C:0.06, G:0.43, T:0.01
Consensus pattern (24 bp):
AGGAAAGAGGAGGAAGAAGCCAGG
Found at i:1409 original size:30 final size:30
Alignment explanation
Indices: 1365--1465 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 30
1355 AAATTGAAAG
*
1365 GGAAAG-GAAGGAAGAGGAAGAAGCCAGGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
*
1394 GGAAAGAGGAGGAAGAGG-AG--GCCAGAA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* * * *
1421 AGAAA-A-GA-GAGGAGGAAGAAGCTAAGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* *
1448 GGAAAGCGGAAGAAGAGG
1 GGAAAGAGGAGGAAGAGG
1466 CCCAAAAGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
24 6 0.11
25 4 0.07
26 1 0.02
27 18 0.33
29 10 0.18
30 16 0.29
ACGTcount: A:0.49, C:0.06, G:0.45, T:0.01
Consensus pattern (30 bp):
GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
Found at i:1490 original size:51 final size:54
Alignment explanation
Indices: 1366--1490 Score: 134
Period size: 54 Copynumber: 2.4 Consensus size: 54
1356 AATTGAAAGG
* * *
1366 GAAAG-GAA-GGAAGAGGAAGAAGCCAGGAGGAAAGAGGAGGAAGAGGAGGCCA
1 GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
* * * * *
1418 GAAAGAAAAGAGAGGAGGAAGAAGCTAAGAGGAAAGCGGAAGAAGA-G-GCCCA
1 GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
*
1470 -AAAGAGAAGGGAAGAAGAAGA
1 GAAAGAGAAGGGAAGAGGAAGA
1491 GGAAGCCAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
51 17 0.29
52 9 0.15
53 3 0.05
54 30 0.51
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.01
Consensus pattern (54 bp):
GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
Found at i:1501 original size:24 final size:24
Alignment explanation
Indices: 1474--1667 Score: 99
Period size: 24 Copynumber: 7.6 Consensus size: 24
1464 GGCCCAAAAG
1474 AGAAGG-GAAGAAGAAGAGGAAGCC
1 AGAAGGAG-AGAAGAAGAGGAAGCC
* *
1498 AGAAGGAGAGAGGAAGAGGAAG-A
1 AGAAGGAGAGAAGAAGAGGAAGCC
* * *
1521 AGCTAAGAGAAGAGAAAAAAAGGAGGCC
1 AG--AAG-G-AGAGAAGAAGAGGAAGCC
* *
1549 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1 AGAAGGAGAGAAGAAGA-G--GAAGC---C
* *
1579 AGAAGGAGAGAGGAAGAGGAAG-A
1 AGAAGGAGAGAAGAAGAGGAAGCC
* *
1602 AGCTAAGAGAAGAGAAGAAAAGGAGGCC
1 AG--AAG-G-AGAGAAGAAGAGGAAGCC
* *
1630 AGAAGGAGAGAGGAAGAGGATGCTC
1 AGAAGGAGAGAAGAAGAGGAAGC-C
1655 -GAAGGAGAGAAGA
1 AGAAGGAGAGAAGA
1668 GGAAGAGGGA
Statistics
Matches: 131, Mismatches: 21, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
23 4 0.03
24 53 0.40
25 11 0.08
26 8 0.06
27 33 0.25
28 4 0.03
29 1 0.01
30 17 0.13
ACGTcount: A:0.50, C:0.06, G:0.42, T:0.03
Consensus pattern (24 bp):
AGAAGGAGAGAAGAAGAGGAAGCC
Found at i:1513 original size:30 final size:29
Alignment explanation
Indices: 1479--1601 Score: 77
Period size: 30 Copynumber: 4.4 Consensus size: 29
1469 AAAAGAGAAG
1479 GGAAGAAGAAGAGGAAGCCAGAAGGAGAGA
1 GGAAGAAGAAGAGGAAG-CAGAAGGAGAGA
* *
1509 GGAAG-AG--GAAGAAGC-TAA-GAGA-A
1 GGAAGAAGAAGAGGAAGCAGAAGGAGAGA
*
1532 GAGAA-AA-AA-AGGAGGCCAGAAGGAGAGA
1 G-GAAGAAGAAGAGGAAG-CAGAAGGAGAGA
* *
1560 GGAAGAGGAAGAAGCTAAG-AGAAGGAGAGA
1 GGAAGAAGAAG-AG-GAAGCAGAAGGAGAGA
*
1590 GGAAGAGGAAGA
1 GGAAGAAGAAGA
1602 AGCTAAGAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 27
0.67 0.07 0.25
Matches are distributed among these distances:
23 2 0.03
24 12 0.17
25 3 0.04
26 3 0.04
27 13 0.18
28 3 0.04
29 5 0.07
30 27 0.38
31 2 0.03
32 2 0.03
ACGTcount: A:0.51, C:0.05, G:0.42, T:0.02
Consensus pattern (29 bp):
GGAAGAAGAAGAGGAAGCAGAAGGAGAGA
Found at i:1514 original size:51 final size:49
Alignment explanation
Indices: 1471--1583 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 49
1461 AGAGGCCCAA
* *
1471 AAGAGAAGGGAAGAAGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGC
1 AAGAGAAGAGAA-AA-AA-AGGAAGCCAGAAGGAGAGAGGAAGAGGAACAA-C
* *
1524 TAAGAGAAGAGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGC
1 -AAGAGAAGAGAAAAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAACAA-C
1575 TAAGAGAAG
1 -AAGAGAAG
1584 GAGAGAGGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 42 0.74
52 2 0.04
53 2 0.04
54 11 0.19
ACGTcount: A:0.52, C:0.05, G:0.41, T:0.02
Consensus pattern (49 bp):
AAGAGAAGAGAAAAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAACAAC
Found at i:1547 original size:81 final size:82
Alignment explanation
Indices: 1405--1646 Score: 259
Period size: 81 Copynumber: 3.0 Consensus size: 82
1395 GAAAGAGGAG
* * * * ** *
1405 GAAGAGGAGGCCAGAAAGA-AAAGAGAGGAGGAAGAAGCTAAGAGGAA-AGCGGAAGAA-GAGGC
1 GAAGAGGAAGCCAGAAGGAGAGAG-GAAGAGGAAGAAGCTAAGA-GAAGAG-AAAAAAAGGAGGC
1467 CCAAAA-GAGA-AGGGAAGAA
63 CCAAAAGGAGAGA-GGAAGAA
1486 GAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGG-CCA
1 GAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCCCA
* *
1550 GAAGGAGAGAGGAAGAG
66 AAAGGAGAGAGGAAGAA
* *
1567 GAAGAAGCTAAG--AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAGAAAAGGAGG-C
1 GAAG-AG-GAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCC
*
1629 CAGAAGGAGAGAGGAAGA
64 CAAAAGGAGAGAGGAAGA
1647 GGATGCTCGA
Statistics
Matches: 143, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
80 12 0.08
81 122 0.85
82 6 0.04
83 3 0.02
ACGTcount: A:0.51, C:0.07, G:0.41, T:0.02
Consensus pattern (82 bp):
GAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCCCA
AAAGGAGAGAGGAAGAA
Found at i:1602 original size:30 final size:30
Alignment explanation
Indices: 1549--1613 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
1539 AAAGGAGGCC
1549 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1579 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1609 AGAAG
1 AGAAG
1614 AGAAGAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.43, T:0.03
Consensus pattern (30 bp):
AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
Found at i:1647 original size:81 final size:81
Alignment explanation
Indices: 1498--1649 Score: 295
Period size: 81 Copynumber: 1.9 Consensus size: 81
1488 AGAGGAAGCC
1498 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCCAGAAGGAGAGAGGA
1 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCCAGAAGGAGAGAGGA
1563 AGAGGAAGAAGCTAAG
66 AGAGGAAGAAGCTAAG
*
1579 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAGAAAAGGAGGCCAGAAGGAGAGAGGA
1 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCCAGAAGGAGAGAGGA
1644 AGAGGA
66 AGAGGA
1650 TGCTCGAAGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.51, C:0.05, G:0.42, T:0.02
Consensus pattern (81 bp):
AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGCCAGAAGGAGAGAGGA
AGAGGAAGAAGCTAAG
Done.