Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1416
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: 13315
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Found at i:3794 original size:14 final size:13
Alignment explanation
Indices: 3770--3799 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3760 TTAAATTACG
3770 ATGTGATTAAATC
1 ATGTGATTAAATC
3783 ATGTGCATTAAATC
1 ATGTG-ATTAAATC
3797 ATG
1 ATG
3800 CTCTATGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTGATTAAATC
Found at i:4132 original size:39 final size:39
Alignment explanation
Indices: 3928--4150 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
3918 TTGAATGCTG
* * * * * *
3928 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
3968 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
4008 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
4048 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
4088 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
4127 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
4151 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:4170 original size:79 final size:80
Alignment explanation
Indices: 4008--4185 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
3998 AGATACAAGT
* * * *
4008 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
4073 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
4088 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
4152 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
4167 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
4186 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:11894 original size:40 final size:38
Alignment explanation
Indices: 11857--12033 Score: 169
Period size: 39 Copynumber: 4.5 Consensus size: 38
11847 ATATCCGGAC
11857 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAGTTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAA--TCCGGGT
* *
11897 TAAGCCCCGAAGGCCTTTGTGCGAGATACTAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAATCCGGGT
* * *
11936 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACT-AATCCGGGT
* * * *
11976 TAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACT-AATCCGGGT
*
12015 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
12034 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
39 64 0.54
40 53 0.45
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAATCCGGGT
Found at i:11945 original size:39 final size:39
Alignment explanation
Indices: 11810--12033 Score: 206
Period size: 40 Copynumber: 5.7 Consensus size: 39
11800 TTGAATGCTG
* *
11810 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTA-A
*
11850 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAA
* * *
11888 GTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAA
1 --TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
* * * *
11929 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AA
* * *
11969 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AA
* *
12008 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
12034 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
38 1 0.01
39 66 0.42
40 77 0.49
41 12 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
Found at i:11950 original size:79 final size:79
Alignment explanation
Indices: 11863--12033 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
11853 GGACTAAGAT
* *
11863 CCGAAGGCATTTGTGCGAGATA-CAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAA-ATCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
11927 -AATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * *
11942 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
12007 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
12021 CCGAAGGCATTTG
1 CCGAAGGCATTTG
12034 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 13 0.17
79 63 0.81
80 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:12051 original size:79 final size:79
Alignment explanation
Indices: 11890--12066 Score: 189
Period size: 79 Copynumber: 2.3 Consensus size: 79
11880 AGATACAAGT
* * * *
11890 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAACCGGGCTAAGTCCCGAAGGCATTCG
** * *
11955 TGCGAGTTATTAAA
66 AACGAGTGACTAAA
* * * *
11969 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACT-AAACCGGGCTAAGTCCCGAAGGCATTC
*
12033 GAACGAG-GAGCTATA
65 GAACGAGTGA-CTAAA
*
12048 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
12067 TACGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 29 0.35
79 53 0.65
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Done.