Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold601
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: 25605
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1641 original size:20 final size:20
Alignment explanation
Indices: 1612--1665 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1602 AGTTTTTCCC
*
1612 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
1632 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
1652 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
1666 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:1647 original size:30 final size:30
Alignment explanation
Indices: 1612--1685 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
1602 AGTTTTTCCC
1612 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
1642 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
1672 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
1686 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:1675 original size:20 final size:20
Alignment explanation
Indices: 1612--1676 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1602 AGTTTTTCCC
* * * *
1612 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
1632 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
1651 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
1672 AGCTC
1 AGCTC
1677 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:7685 original size:15 final size:15
Alignment explanation
Indices: 7665--7719 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
7655 TATCTTCTTC
7665 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
7680 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAA
7695 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
7710 TTTTTTTTCA
1 TTTTTTTTCA
7720 ACTTGATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:7774 original size:12 final size:12
Alignment explanation
Indices: 7757--7802 Score: 76
Period size: 11 Copynumber: 3.8 Consensus size: 12
7747 ATGGAAACCA
7757 AATTTTTTTTTT
1 AATTTTTTTTTT
7769 AA-TTTTTTTTT
1 AATTTTTTTTTT
7780 AATTTTTTTTTT
1 AATTTTTTTTTT
7792 GAATTTTTTTT
1 -AATTTTTTTT
7803 CGAGAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.34
12 11 0.34
13 10 0.31
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (12 bp):
AATTTTTTTTTT
Found at i:7776 original size:11 final size:11
Alignment explanation
Indices: 7760--7802 Score: 68
Period size: 12 Copynumber: 3.7 Consensus size: 11
7750 GAAACCAAAT
7760 TTTTTTTTTAA
1 TTTTTTTTTAA
7771 TTTTTTTTTAA
1 TTTTTTTTTAA
7782 TTTTTTTTTTGAA
1 -TTTTTTTTT-AA
7795 TTTTTTTT
1 TTTTTTTT
7803 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.37
12 17 0.57
13 2 0.07
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:7777 original size:13 final size:13
Alignment explanation
Indices: 7759--7802 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
7749 GGAAACCAAA
7759 TTTTTTTTTTAA-
1 TTTTTTTTTTAAT
7771 -TTTTTTTTTAAT
1 TTTTTTTTTTAAT
*
7783 TTTTTTTTTGAAT
1 TTTTTTTTTTAAT
7796 TTTTTTT
1 TTTTTTT
7803 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTAAT
Found at i:7787 original size:23 final size:24
Alignment explanation
Indices: 7757--7802 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
7747 ATGGAAACCA
7757 AATTTTTTTTTT-AATTTTTTTTT
1 AATTTTTTTTTTGAATTTTTTTTT
7780 AATTTTTTTTTTGAATTTTTTTT
1 AATTTTTTTTTTGAATTTTTTTT
7803 CGAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (24 bp):
AATTTTTTTTTTGAATTTTTTTTT
Found at i:8173 original size:46 final size:46
Alignment explanation
Indices: 8120--8213 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
8110 CAAAGAAAAG
* *
8120 ACCTCGACCCACTATCTA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
8166 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
8212 AC
1 AC
8214 GCCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:12827 original size:13 final size:11
Alignment explanation
Indices: 12799--12832 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
12789 TACGGTATTG
12799 TAAAAAAAAAT
1 TAAAAAAAAAT
12810 TAAAAAAAAAT
1 TAAAAAAAAAT
12821 TCGAAAAAAAAA
1 T--AAAAAAAAA
12833 AAAATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
13 9 0.43
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (11 bp):
TAAAAAAAAAT
Found at i:12830 original size:16 final size:17
Alignment explanation
Indices: 12811--12866 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
12801 AAAAAAAATT
12811 AAAAAAAAA-TTCGAAAA
1 AAAAAAAAATTTCG-AAA
*
12828 AAAAAAAAATTTTGAAA
1 AAAAAAAAATTTCGAAA
12845 AAAAAAAAATTTC-AAA
1 AAAAAAAAATTTCGAAA
12861 AAAAAA
1 AAAAAA
12867 GTTTGTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 9 0.25
17 24 0.67
18 3 0.08
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAAAAAATTTCGAAA
Found at i:12833 original size:17 final size:17
Alignment explanation
Indices: 12811--12866 Score: 78
Period size: 18 Copynumber: 3.3 Consensus size: 17
12801 AAAAAAAATT
12811 AAAAAAAAATTCGAAAA
1 AAAAAAAAATTCGAAAA
*
12828 AAAAAAAAATTTTGAAAA
1 AAAAAAAAA-TTCGAAAA
*
12846 AAAAAAAATTTC-AAAA
1 AAAAAAAAATTCGAAAA
12862 AAAAA
1 AAAAA
12867 GTTTGTATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.26
17 11 0.31
18 15 0.43
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAAAAAATTCGAAAA
Found at i:12954 original size:32 final size:31
Alignment explanation
Indices: 12904--12984 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 31
12894 TGTATTTAGT
* *
12904 ATTGAAGAAAAAAAAAGAAAAAAAAATTCGAA
1 ATTGAAAAAAAAAAAAGAAAAAAAAA-TCAAA
12936 ATT-AAAAAAAAAAGAAGAAAAAAAAATCAAA
1 ATTGAAAAAAAAAA-AAGAAAAAAAAATCAAA
12967 ATTGAAAAAAAAAAAAGA
1 ATTGAAAAAAAAAAAAGA
12985 GTGATTGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
31 20 0.44
32 25 0.56
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.11
Consensus pattern (31 bp):
ATTGAAAAAAAAAAAAGAAAAAAAAATCAAA
Found at i:12967 original size:20 final size:20
Alignment explanation
Indices: 12943--12981 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12933 GAAATTAAAA
*
12943 AAAAAAGAAGAAAAAAAAATC
1 AAAATAGAA-AAAAAAAAATC
*
12964 AAAATTGAAAAAAAAAAA
1 AAAATAGAAAAAAAAAAA
12982 AGAGTGATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAATAGAAAAAAAAAAATC
Found at i:12967 original size:21 final size:21
Alignment explanation
Indices: 12943--12982 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12933 GAAATTAAAA
*
12943 AAAAAAGAAGAAAAAAAAATC
1 AAAAAAGAAAAAAAAAAAATC
**
12964 AAAATTGAAAAAAAAAAAA
1 AAAAAAGAAAAAAAAAAAA
12983 GAGTGATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAAAATC
Found at i:13900 original size:21 final size:20
Alignment explanation
Indices: 13871--13916 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
13861 AATCTTGAAT
*
13871 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
13892 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
13912 GAAAA
1 GAAAA
13917 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:13943 original size:12 final size:12
Alignment explanation
Indices: 13923--13958 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
13913 AAAAAAGAAT
*
13923 TTGAGATTGAGA
1 TTGATATTGAGA
*
13935 TTGATATTGATA
1 TTGATATTGAGA
13947 TTGATATTGAGA
1 TTGATATTGAGA
13959 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:19558 original size:70 final size:70
Alignment explanation
Indices: 19445--19577 Score: 230
Period size: 70 Copynumber: 1.9 Consensus size: 70
19435 TTAAATCAGC
19445 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
1 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
19510 ACAGT
66 ACAGT
* * * *
19515 AGCAATAAAGGAGGTTTTGGCTGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTGTT
1 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTT
19578 GGGCATGCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.30
Consensus pattern (70 bp):
AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
ACAGT
Found at i:20549 original size:21 final size:21
Alignment explanation
Indices: 20523--20585 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
20513 TTGGTATTTG
20523 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
20544 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
20565 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
20586 ATGGTCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Done.