Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2608
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: 23720
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:6486 original size:20 final size:20
Alignment explanation
Indices: 6433--6486 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
6423 AAACCCTTGT
*
6433 ATGTATCAATACACATCCAG
1 ATGTATCAATACATATCCAG
6453 ATGTATCAATACATATCCAG
1 ATGTATCAATACATATCCAG
*
6473 ATGTATCGATACAT
1 ATGTATCAATACAT
6487 TATGCTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
ATGTATCAATACATATCCAG
Found at i:6914 original size:13 final size:13
Alignment explanation
Indices: 6896--6984 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
6886 CATAAAGTGT
6896 TGTATCGATACAA
1 TGTATCGATACAA
6909 TGTATCGATACATAA
1 TGTATCGATAC--AA
6924 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
6941 TGTATCGATACATAA
1 TGTATCGATAC--AA
6956 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
6973 TGTATCGATACA
1 TGTATCGATACA
6985 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6931 original size:32 final size:32
Alignment explanation
Indices: 6876--7005 Score: 242
Period size: 32 Copynumber: 4.0 Consensus size: 32
6866 TTTAACGATT
6876 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
6909 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
6941 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
6973 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
7005 T
1 T
7006 ATAAGCTATT
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 83 0.86
33 13 0.14
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:6933 original size:19 final size:18
Alignment explanation
Indices: 6874--7003 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
6864 ATTTTAACGA
6874 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
6893 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
6909 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
6925 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
6941 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
6957 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
6973 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
6989 TTTTGTATCGATACA
1 -TTTGTATCGATACA
7004 ATATAAGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:7073 original size:19 final size:19
Alignment explanation
Indices: 7022--7076 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
7012 TATTGCCAAA
*
7022 AAATGTATCGATAAATTTC
1 AAATGTATCGATACATTTC
7041 AAATGTATCGATACATTTC
1 AAATGTATCGATACATTTC
7060 AAATGTATCGATACATT
1 AAATGTATCGATACATT
7077 GTATCGATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (19 bp):
AAATGTATCGATACATTTC
Found at i:7081 original size:13 final size:13
Alignment explanation
Indices: 7063--7087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7053 ACATTTCAAA
7063 TGTATCGATACAT
1 TGTATCGATACAT
7076 TGTATCGATACA
1 TGTATCGATACA
7088 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10645 original size:36 final size:36
Alignment explanation
Indices: 10600--10676 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
10590 TTTATTGTTA
*
10600 TTATTTTTCGAAAGCTCTTTTTTATTTGTTTTGAGC
1 TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
10636 TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
1 TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
10672 TTATT
1 TTATT
10677 CCTTCACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.58
Consensus pattern (36 bp):
TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
Found at i:17103 original size:42 final size:42
Alignment explanation
Indices: 17032--18130 Score: 913
Period size: 42 Copynumber: 26.2 Consensus size: 42
17022 ATTAAACTTT
*
17032 TGGAGACTTTCCTT-CCTTAGTCTGCCTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * *
17073 TGGAAACTTTCTTTCCCTTAGTCTGTCTGTCAGCTTTGACAC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * *
17115 TGGAGACTTTCCTACCCTTAGTCTACCTATCAGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * *
17157 TAGAGACTTTCTTTCCCTTAGTTTGCTTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
**
17199 TGGAGACTTTCCTTCCCTTAGTCCACCTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
17241 TAGAGACTTT-TTTCCCCTTAGTCTGCCTGTCAGCTTTGACCC
1 TGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACCC
17283 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * ** *
17325 TAGAGACTTTCCTTCCCTTAGTCTGCCTATTAGCTTTGTCGCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGAC-CC
*
17368 TGGAGACTTTTCTAT-CCTTAGTCTGCCTGTCGGCTTTGA-CC
1 TGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
17409 TCGGAGACTTTCCTTCCCTTAGTCTACCTGTTGGCTTTGACCT
1 T-GGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * *
17452 TGGAGACTTTTCTGCCTTTAGCCTGCCTGTTGGCTTTAACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * * * *
17494 TAGAGATTTTCATGCCCTCACTTTGCCTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * *
17536 TGGAGACTTTTCTACCCTTAGTTTGCTTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
17578 TGGAGA-TTGCCTT--CTCAGTCTGCCTATCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * ** *
17617 TGGAGACTTTCCTGCCCTCAGTCTGCCTATCGATTTTGACGC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * *
17659 TAGATACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * *
17701 TGGAGAC-TGCC-TCATCTAAAGTTTGCTTGTCGACTTTGACCC
1 TGGAGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * * * * *
17743 TGAAGACTTTCCTACCCTCAGTCTGCTTGTCAGCTCTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
17785 TGGAGACTTT-CTTACCCTCAGTCTACCTGTCGACTTTGACCC
1 TGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACCC
* ** * * *
17827 TGGAGACTGT-CTTATCTAAAGTCTGCTTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCT-TAGTCTGCCTGTCGGCTTTGACCC
* * *
17869 TGGAGACTTTCCTAT-CCTTAAG-CTGCTTGTCGACTTTGACCT
1 TGGAGACTTTCCT-TCCCTT-AGTCTGCCTGTCGGCTTTGACCC
* * * *
17911 TGGAGACTTTCCTAT-CCTTAATCTGCTTGTTGGCTTTGACCT
1 TGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * *
17953 TGGAGAC-TGCC-TCATCTAAAGTTTGCCTGTTGGCTTTGACCC
1 TGGAGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * * *
17995 TGGAGACTTTCCTACCCTCAATCTGCCTGTTGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * * * *
18037 TGGAGAC-TGCC-TCATCTAAAGTTTGCCTATCGGCGTTGATCT
1 TGGAGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * *
18079 TGGAGACTTT-CTTACCCTCAGTTTGCCTGCCAGCTTTGACCC
1 TGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACCC
18121 TGGAGACTTT
1 TGGAGACTTT
18131 TTTACTTTTT
Statistics
Matches: 853, Mismatches: 174, Indels: 61
0.78 0.16 0.06
Matches are distributed among these distances:
39 29 0.03
40 7 0.01
41 42 0.05
42 713 0.84
43 57 0.07
44 5 0.01
ACGTcount: A:0.15, C:0.29, G:0.20, T:0.37
Consensus pattern (42 bp):
TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
Found at i:18165 original size:42 final size:43
Alignment explanation
Indices: 18099--18182 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
18089 CTTACCCTCA
* * *
18099 GTTTGCCTGCCAGCTTTGACCCT-GGAGACTTTTTTACTTTTTT
1 GTTTGCCTGCCAGCTTTGAACCTGGGAGAATCTTTT-CTTTTTT
**
18142 GTTTGCCTGTTAGCTTT-AACCTGGGAGAATCTTTTCTTTTT
1 GTTTGCCTGCCAGCTTTGAACCTGGGAGAATCTTTTCTTTTT
18183 ACCTGTCGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 10 0.29
43 25 0.71
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (43 bp):
GTTTGCCTGCCAGCTTTGAACCTGGGAGAATCTTTTCTTTTTT
Found at i:18662 original size:14 final size:13
Alignment explanation
Indices: 18645--18707 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
18635 AAAAAACAAA
18645 AAATATAAAAAAT
1 AAATATAAAAAAT
18658 CAAAT-T-AAAAAT
1 -AAATATAAAAAAT
*
18670 AAATAATAAATAAT
1 AAAT-ATAAAAAAT
*
18684 AAATAATTAAAAA-
1 AAAT-ATAAAAAAT
*
18697 AAATTTAAAAA
1 AAATATAAAAA
18708 GAGGGGAGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 4 0.10
12 11 0.27
13 6 0.15
14 20 0.49
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATATAAAAAAT
Found at i:18687 original size:25 final size:24
Alignment explanation
Indices: 18617--18689 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
18607 TATTCAATGT
*
18617 AAAATATAATAATAAGTAA-AAA-A
1 AAAATA-AATAATAAATAATAAATA
*
18640 ACAAA-AAAT-ATAAAAAATCAAATTA
1 A-AAATAAATAATAAATAAT-AAA-TA
18665 AAAATAAATAATAAATAATAAATA
1 AAAATAAATAATAAATAATAAATA
18689 A
1 A
18690 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 5 0.12
24 9 0.22
25 9 0.22
26 8 0.20
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (24 bp):
AAAATAAATAATAAATAATAAATA
Found at i:18799 original size:43 final size:41
Alignment explanation
Indices: 18738--18820 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
18728 AGGATTTGTA
* * * *
18738 GCCACCTAATTGACTTAGGTGGCATTGCATTGCATTGCATGCT
1 GCCACCTAAATCAATTAGGTGGCAATGCA-TGCATT-CATGCT
18781 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGC
1 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGC
18821 ATGAAATTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 6 0.17
43 25 0.69
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGCT
Found at i:18993 original size:20 final size:20
Alignment explanation
Indices: 18968--19008 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18958 TCATATGAAA
18968 ATAAGATTGGTGTAAACAGC
1 ATAAGATTGGTGTAAACAGC
18988 ATAAGATTGGTGTAAACAGC
1 ATAAGATTGGTGTAAACAGC
19008 A
1 A
19009 GCAAATAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
ATAAGATTGGTGTAAACAGC
Found at i:19487 original size:49 final size:48
Alignment explanation
Indices: 19396--19490 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 48
19386 AGTGACCACC
* *
19396 GCAACCTCCAGCAGCCCAGTAACTCCCACGACAGCCTTCAACAGCTAA
1 GCAACCTCCAGCAGCCCAGCAACTCCCACGACAGCCTCCAACAGCTAA
* * * * *
19444 GCAACTTCCAGTAGCTCCAGCAACTTCCATGGCAGCCTCCAACAGCT
1 GCAACCTCCAGCAGC-CCAGCAACTCCCACGACAGCCTCCAACAGCT
19491 CCTACGACAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 13 0.33
49 26 0.67
ACGTcount: A:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (48 bp):
GCAACCTCCAGCAGCCCAGCAACTCCCACGACAGCCTCCAACAGCTAA
Found at i:19583 original size:30 final size:31
Alignment explanation
Indices: 19543--19628 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
19533 TATAGCTCCT
*
19543 ACAGTAACTTTCAGCAGCTCCCACAGC-TCC
1 ACAGCAACTTTCAGCAGCTCCCACAGCTTCC
* *
19573 ATAGCAACTTTCAGCAGCT-CTAGCAGCTTCC
1 ACAGCAACTTTCAGCAGCTCCCA-CAGCTTCC
* * *
19604 ACAGCAACCTCCAACAGCTCCCACA
1 ACAGCAACTTTCAGCAGCTCCCACA
19629 ACAGCCTCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
29 2 0.04
30 21 0.47
31 20 0.44
32 2 0.04
ACGTcount: A:0.29, C:0.40, G:0.13, T:0.19
Consensus pattern (31 bp):
ACAGCAACTTTCAGCAGCTCCCACAGCTTCC
Found at i:19622 original size:22 final size:22
Alignment explanation
Indices: 19596--19686 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 22
19586 GCAGCTCTAG
19596 CAGCTTCCACAGCAACCTCCAA
1 CAGCTTCCACAGCAACCTCCAA
* * * *
19618 CAGCTCCCACAACAGCCTCCAG
1 CAGCTTCCACAGCAACCTCCAA
* *
19640 CAGCTT--A-A-CAATC-CCAGG
1 CAGCTTCCACAGCAACCTCCA-A
* *
19658 CAGCTCCCACAGCAACTTCCAA
1 CAGCTTCCACAGCAACCTCCAA
19680 CAGCTTC
1 CAGCTTC
19687 AGCAGCTTCC
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 3 0.06
18 9 0.18
19 1 0.02
20 2 0.04
21 1 0.02
22 32 0.63
23 3 0.06
ACGTcount: A:0.30, C:0.44, G:0.12, T:0.14
Consensus pattern (22 bp):
CAGCTTCCACAGCAACCTCCAA
Found at i:19730 original size:31 final size:31
Alignment explanation
Indices: 19657--19746 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
19647 ACAATCCCAG
* * * * *
19657 GCAGCTCCCACAGCAACTTCCAACAGCTTCA
1 GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
*
19688 GCAGCTTCCACGGTAGCCTCCAGCAGCTTCA
1 GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
19719 GCAGCTCCCACGGTAGCCTCCAGCAGCT
1 GCAGCTCCCACGGTAGCCTCCAGCAGCT
19747 CCCACGACAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.22, C:0.41, G:0.20, T:0.17
Consensus pattern (31 bp):
GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
Found at i:19745 original size:22 final size:22
Alignment explanation
Indices: 19717--19783 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
19707 CCAGCAGCTT
**
19717 CAGCAGCTCCCACGGTAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
19739 CAGCAGCTCCCACGACAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
*
19761 TAGCAGCT--CA-G-CAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
19779 CAGCA
1 CAGCA
19784 ACTTCCAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 2 0.05
22 27 0.66
ACGTcount: A:0.22, C:0.45, G:0.21, T:0.12
Consensus pattern (22 bp):
CAGCAGCTCCCACGACAGCCTC
Done.