Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2953
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: 52649
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:978 original size:13 final size:13
Alignment explanation
Indices: 960--985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
950 AAGTTTTATT
960 TTTATTTATTTTA
1 TTTATTTATTTTA
973 TTTATTTATTTTA
1 TTTATTTATTTTA
986 CTTTGGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:6551 original size:32 final size:32
Alignment explanation
Indices: 6510--6573 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6500 CCTACTATAA
6510 TGACCACGCCCTTTGCACTTAAAACATTCAAC
1 TGACCACGCCCTTTGCACTTAAAACATTCAAC
6542 TGACCACGCCCTTTGCACTTAAAACATTCAAC
1 TGACCACGCCCTTTGCACTTAAAACATTCAAC
6574 CTCACGATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.09, T:0.25
Consensus pattern (32 bp):
TGACCACGCCCTTTGCACTTAAAACATTCAAC
Found at i:9248 original size:15 final size:14
Alignment explanation
Indices: 9225--9258 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
9215 TTGATTGGGC
*
9225 TTGGAATCTTCTTGA
1 TTGGGATCTTCTT-A
9240 TTGGGATCTTCTTA
1 TTGGGATCTTCTTA
9254 TTGGG
1 TTGGG
9259 CCTTGCCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.15, C:0.12, G:0.26, T:0.47
Consensus pattern (14 bp):
TTGGGATCTTCTTA
Found at i:12547 original size:19 final size:19
Alignment explanation
Indices: 12523--12562 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12513 AGCTCCCATG
12523 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
12542 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
12561 TA
1 TA
12563 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:13885 original size:30 final size:30
Alignment explanation
Indices: 13851--13947 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
13841 AGCTCACTCC
13851 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
13881 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
13911 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
13941 TAGCTCA
1 TAGCTCA
13948 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:17049 original size:13 final size:13
Alignment explanation
Indices: 17031--17055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17021 GTATTGATCA
17031 TGTGTTCACACCT
1 TGTGTTCACACCT
17044 TGTGTTCACACC
1 TGTGTTCACACC
17056 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:19163 original size:47 final size:47
Alignment explanation
Indices: 19094--19189 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
19084 GCACTTGGGT
*
19094 GGCTTGGATACATGCATATGGATTAATGTCATACATTTCTTTTGGAC
1 GGCTTGGATACATGCATATGGATTAATGTCATACATTTCCTTTGGAC
19141 GGCTTGGATACATGCATATGGATTAATGTCATACATTTCCTTTGGAC
1 GGCTTGGATACATGCATATGGATTAATGTCATACATTTCCTTTGGAC
19188 GG
1 GG
19190 TACACATGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (47 bp):
GGCTTGGATACATGCATATGGATTAATGTCATACATTTCCTTTGGAC
Found at i:20238 original size:14 final size:14
Alignment explanation
Indices: 20221--20260 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20211 CGAATGGAAT
*
20221 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
20235 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
20249 GATATGAACAAA
1 GGTAGGAACAAA
20261 TTTCTCGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:23686 original size:20 final size:20
Alignment explanation
Indices: 23661--23714 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
23651 TGTGGTTCAA
*
23661 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
23681 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
23701 CTCATTCAAGCTCA
1 CTCATTCGAGCTCA
23715 GTTTAACTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:24098 original size:45 final size:45
Alignment explanation
Indices: 24048--24241 Score: 271
Period size: 45 Copynumber: 4.3 Consensus size: 45
24038 GAACGGCATG
* *
24048 AAATTAAGGAAGCATTTGACCAACATCATGCTTAATTTATGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* *
24093 AAATTAAGGAAGCACTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
24138 AATTTGAGGAAACATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
24183 AATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
24228 AAATTGAGGAAGCA
1 AAATTAAGGAAGCA
24242 CCATGGCCGA
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (45 bp):
AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
Found at i:26812 original size:23 final size:22
Alignment explanation
Indices: 26761--26812 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
26751 CCTCGTCTTT
*
26761 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
26783 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
26806 TTCTTTT
1 TTCTTTT
26813 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:27453 original size:22 final size:22
Alignment explanation
Indices: 27423--27466 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27413 TTTGGTATTT
27423 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27445 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27467 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:34037 original size:23 final size:22
Alignment explanation
Indices: 33985--34037 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33975 TCCACGTCTT
*
33985 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
34007 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
34030 TTTCTTTT
1 TTTCTTTT
34038 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:37401 original size:17 final size:17
Alignment explanation
Indices: 37379--37427 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
37369 TTTTCATTTC
37379 TTTTTTTGAATTTTCTT
1 TTTTTTTGAATTTTCTT
*
37396 TTTTTTT-CATCTTTCTT
1 TTTTTTTGAAT-TTTCTT
* *
37413 TTCTTTTGTATTTTC
1 TTTTTTTGAATTTTC
37428 GCTCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTTTTGAATTTTCTT
Found at i:39969 original size:22 final size:22
Alignment explanation
Indices: 39939--39982 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39929 TTTGGTATTT
39939 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39961 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39983 TGGTTCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:48574 original size:24 final size:25
Alignment explanation
Indices: 48521--48574 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
48511 AACAAATTCT
* *
48521 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
48546 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
48569 TTTTTT
1 TTTTTT
48575 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:50859 original size:21 final size:21
Alignment explanation
Indices: 50833--50874 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50823 TATGCAATTT
50833 TTTTTTTTCAAATTTTTTTTC
1 TTTTTTTTCAAATTTTTTTTC
* *
50854 TTTTTTTTCGATTTTTTTTTC
1 TTTTTTTTCAAATTTTTTTTC
50875 GAAACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTTCAAATTTTTTTTC
Found at i:50891 original size:11 final size:12
Alignment explanation
Indices: 50833--50898 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
50823 TATGCAATTT
*
50833 TTTTTTTTCAAA
1 TTTTTTTTCAAC
50845 TTTTTTTT---C
1 TTTTTTTTCAAC
* *
50854 TTTTTTTTCGAT
1 TTTTTTTTCAAC
50866 TTTTTTTTCGAAAC
1 TTTTTTTTC--AAC
50880 TTTTTTTT-AAC
1 TTTTTTTTCAAC
50891 TTTTTTTT
1 TTTTTTTT
50899 TCGAAGCTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.18
11 11 0.24
12 17 0.38
14 9 0.20
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAC
Done.