Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3058
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: 17860
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:873 original size:36 final size:36
Alignment explanation
Indices: 826--948 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 36
816 TTGGTTATCT
* *
826 GACTAGAGCTGGGCTCAATAATTTGTCGATTCGTTC
1 GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC
* * * * *
862 GACTAGTGCTGGGCAGAACT-A-TCGTCGGTT-ATCC
1 GACTAGTGCTGGGCACAA-TAATTTGTCGATTCGTTC
** * * *
896 GGTTAGTGCTGAGCACAATAATTTTTCAATTCGTTC
1 GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC
932 GACTAGTGCTGGGCACA
1 GACTAGTGCTGGGCACA
949 CCAATGATTT
Statistics
Matches: 63, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
33 1 0.02
34 17 0.27
35 12 0.19
36 32 0.51
37 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (36 bp):
GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC
Found at i:1836 original size:28 final size:28
Alignment explanation
Indices: 1805--1867 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
1795 TCTCAGCTGT
*
1805 GTGTGACACACGGCTAGGCGACATAGCC
1 GTGTGACACACAGCTAGGCGACATAGCC
* * *
1833 GTGTATGACACACAGTTAGGCGACATGGCT
1 GTG--TGACACACAGCTAGGCGACATAGCC
1863 GTGTG
1 GTGTG
1868 TTTATTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 5 0.17
30 24 0.83
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (28 bp):
GTGTGACACACAGCTAGGCGACATAGCC
Found at i:5448 original size:18 final size:18
Alignment explanation
Indices: 5420--5472 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
5410 TTGGCCAATT
*
5420 CAGTAACAGTAAACAGTG
1 CAGTAATAGTAAACAGTG
*
5438 TAGTAATAGTAAACAGTG
1 CAGTAATAGTAAACAGTG
5456 CAGT-ATCAGTAAACAGT
1 CAGTAAT-AGTAAACAGT
5473 ATGCAAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (18 bp):
CAGTAATAGTAAACAGTG
Found at i:9935 original size:24 final size:24
Alignment explanation
Indices: 9907--9958 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9897 CCCATTTTTT
*
9907 CCTCCCCTAATCTCTCCTAAAATC
1 CCTCCCCAAATCTCTCCTAAAATC
* * *
9931 CCTCCTCAAATCTCTCTTCAAATC
1 CCTCCCCAAATCTCTCCTAAAATC
9955 CCTC
1 CCTC
9959 AACTGATCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (24 bp):
CCTCCCCAAATCTCTCCTAAAATC
Found at i:9951 original size:12 final size:12
Alignment explanation
Indices: 9915--9954 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9905 TTCCTCCCCT
*
9915 AATCTCTCCTAA
1 AATCTCTCCTCA
*
9927 AATCCCTCCTCA
1 AATCTCTCCTCA
*
9939 AATCTCTCTTCA
1 AATCTCTCCTCA
9951 AATC
1 AATC
9955 CCTCAACTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.33
Consensus pattern (12 bp):
AATCTCTCCTCA
Found at i:14081 original size:13 final size:13
Alignment explanation
Indices: 14065--14098 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
14055 CACACGACCA
*
14065 TGTAACACAGCCG
1 TGTAACACAACCG
14078 TGTAACACAACCG
1 TGTAACACAACCG
14091 TGTAACAC
1 TGTAACAC
14099 GCCCATGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (13 bp):
TGTAACACAACCG
Found at i:16697 original size:46 final size:46
Alignment explanation
Indices: 16644--16780 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
16634 ATATATAACA
* * * *
16644 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
16690 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
16736 TAACTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
16781 ATACATGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:16814 original size:47 final size:47
Alignment explanation
Indices: 16754--16974 Score: 352
Period size: 47 Copynumber: 4.7 Consensus size: 47
16744 ACACATTTCG
* * * **
16754 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
16801 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
16848 CATTGGCCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
16895 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
16942 CATTGGCCATTTGGCCTTATCACACATACGCAT
1 CATTGGCCATTCGGCCTTATCACACATACGCAT
16975 CACCCAAACA
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 165 1.00
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:16897 original size:23 final size:23
Alignment explanation
Indices: 16870--16944 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
16860 GGCCTTATCG
16870 CACATACGCATGTTCACATTCAT
1 CACATACGCATGTTCACATTCAT
** * *
16893 CACATTGGCCA--TTCGGCCTT-AT
1 CACATACG-CATGTTC-ACATTCAT
16915 CACACATACGCATGTTCACATTCAT
1 --CACATACGCATGTTCACATTCAT
16940 CACAT
1 CACAT
16945 TGGCCATTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 5 0.14
23 16 0.43
24 11 0.30
25 5 0.14
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.29
Consensus pattern (23 bp):
CACATACGCATGTTCACATTCAT
Done.