Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold563
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: 19018
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Found at i:1382 original size:48 final size:47
Alignment explanation
Indices: 1311--1493 Score: 204
Period size: 48 Copynumber: 3.7 Consensus size: 47
1301 CGAAGCTATC
*
1311 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAAT
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT-AT
* * * * *
1359 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTT
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATAT
** *
1408 TCGGGTATGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAATTAT
1 T--GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA-TAT
* *
1458 CCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 -TGGTACACATAGTAGCCTGCACTTAGTACTACACA
1494 CGTGACCTCA
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
48 36 0.33
49 35 0.32
50 6 0.05
51 33 0.30
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (47 bp):
TGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAT
Found at i:1425 original size:99 final size:100
Alignment explanation
Indices: 1312--1498 Score: 331
Period size: 99 Copynumber: 1.9 Consensus size: 100
1302 GAAGCTATCT
* *
1312 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAAT-TGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
1376 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* *
1411 GGTATGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
1476 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
1499 CCTCACAATA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
99 44 0.53
100 39 0.47
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:1444 original size:51 final size:49
Alignment explanation
Indices: 1307--1500 Score: 219
Period size: 49 Copynumber: 3.9 Consensus size: 49
1297 TAGCCGAAGC
* * * *
1307 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * * *
1356 AAT-TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* * ** * * *
1406 TTTCGGGTATGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
*
1455 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
1501 TCACAATAGT
Statistics
Matches: 118, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
48 36 0.31
49 44 0.37
50 5 0.04
51 33 0.28
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:3979 original size:15 final size:15
Alignment explanation
Indices: 3923--3987 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
3913 TAAAGATAAC
*
3923 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
3937 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
3952 GAA-AAACCCAGAATA
1 -AAGAAATCCAGAATA
3967 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
3982 AAGAAA
1 AAGAAA
3988 CCCAAGATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 11 0.26
15 29 0.67
16 3 0.07
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:3989 original size:30 final size:31
Alignment explanation
Indices: 3923--3991 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
3913 TAAAGATAAC
*
3923 AAGAAAACC-GAATAAAGAAATCCAAGATAG
1 AAGAAACCCAGAATAAAGAAATCCAAGATAG
3953 AA-AAACCCAGAATAAAGAAATCC-AGAATA-
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATAG
3982 AAGAAACCCA
1 AAGAAACCCA
3992 AGATACGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.61, C:0.17, G:0.13, T:0.09
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATAG
Found at i:7025 original size:49 final size:49
Alignment explanation
Indices: 6952--7139 Score: 250
Period size: 49 Copynumber: 3.8 Consensus size: 49
6942 TAGCCGAAGC
*
6952 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * * *
7001 AATCTGGTACACCTAGTAGCCTGCACTTATTACTACACACGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * *
7052 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* *
7101 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
7140 CGTGACCTCA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 76 0.65
50 2 0.02
51 39 0.33
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:7071 original size:100 final size:100
Alignment explanation
Indices: 6957--7144 Score: 340
Period size: 100 Copynumber: 1.9 Consensus size: 100
6947 GAAGCTATCT
*
6957 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACCTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACCTAGTAGCC
*
7022 TGCACTTATTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* *
7057 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACCTAGTAGCC
7122 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
7145 CCTCACAATA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACCTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:9647 original size:15 final size:15
Alignment explanation
Indices: 9595--9648 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
9585 TAAAGATAAC
*
9595 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
*
9609 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
9624 GAA-AAACCCAGAATA
1 -AAGAAACCCAGAATA
9639 AAGAAACCCA
1 AAGAAACCCA
9649 AGATACGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.33
15 19 0.58
16 3 0.09
ACGTcount: A:0.61, C:0.19, G:0.13, T:0.07
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:12696 original size:51 final size:49
Alignment explanation
Indices: 12631--12776 Score: 168
Period size: 49 Copynumber: 2.9 Consensus size: 49
12621 TAGCCGAAGC
* *
12631 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* * * * *
12682 TTTCGGGTACGCATAGTAGCCTGCATTTAGTACTACACATGCGACCAAT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * *
12731 TATCCGGTACACGTAGTAGTGC-GCACTTAGTACTACACACGTGACC
1 TATCCGGTACGCATAGTAG-CCTGCACTTAGTACTACACACGTGACC
12777 TCACAATAGT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 39 0.49
50 2 0.03
51 39 0.49
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (49 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:16886 original size:28 final size:28
Alignment explanation
Indices: 16854--16923 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
16844 ATAGTAAGTC
16854 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
16882 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
16910 CGCACACTTAGTGC
1 CGCACACTTAGTGC
16924 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Done.