Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3032
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: 52051
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:14591 original size:28 final size:29
Alignment explanation
Indices: 14538--14597 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
14528 AAAGCATGAC
*
14538 TATGAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
* *
14567 TATGAATGAGA-TTGGGCCTAGTGGGCTA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
14595 TAT
1 TAT
14598 ACATGTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.32
Consensus pattern (29 bp):
TATGAATGAGATTTGGGCCTAATGGGCCA
Found at i:32047 original size:44 final size:42
Alignment explanation
Indices: 31914--32062 Score: 117
Period size: 44 Copynumber: 3.5 Consensus size: 42
31904 AATGCTAATG
* * *
31914 TCCCAGACATGGTCTTACATGT-AATCAAATATCGATGCCACTA
1 TCCCAGAGATGGTCTTACACGTAAATCTAA-ATCGATGCCAC-A
* * * * * **
31957 TCCCAAATAGGGTCTTACAC-AAAAT-TAAATATGATGCCGATG
1 TCCCAGAGATGGTCTTACACGTAAATCTAAAT-CGATGCC-ACA
31999 TCCCAGAGATGGTCTTACACGTAAATCTCAAATCGATGCCAACA
1 TCCCAGAGATGGTCTTACACGTAAATCT-AAATCGATGCC-ACA
32043 TCCCAGACG-TGGTCTTACAC
1 TCCCAGA-GATGGTCTTACAC
32063 AAAATCACAT
Statistics
Matches: 82, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
41 2 0.02
42 25 0.30
43 24 0.29
44 26 0.32
45 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
TCCCAGAGATGGTCTTACACGTAAATCTAAATCGATGCCACA
Found at i:32057 original size:86 final size:85
Alignment explanation
Indices: 31911--32067 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 85
31901 TACAATGCTA
*
31911 ATGTCCCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTATCCCAAATAGGGTCTTACA
1 ATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAAATAGGGTCTTACA
31976 CAAAATTAAATATGATGCCG
66 CAAAATTAAATATGATGCCG
* * * *
31996 ATGTCCCAGAGATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-ATCCCAGA-CGTGGTCT
1 ATGTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTATCCCAAATAG-GGTCT
32058 TACACAAAAT
62 TACACAAAAT
32068 CACATATCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
85 24 0.38
86 35 0.56
87 4 0.06
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (85 bp):
ATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAAATAGGGTCTTACA
CAAAATTAAATATGATGCCG
Found at i:37887 original size:53 final size:53
Alignment explanation
Indices: 37709--37917 Score: 240
Period size: 55 Copynumber: 3.9 Consensus size: 53
37699 ATTAAGGTTT
* * * *
37709 AAGGATACCATATAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTATAAGGC
* * * * *
37764 AAGGAAATCATGTAAGACCATGTCAAGACATGACATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TATAAGGC
* * *
37819 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTTATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTATAAGGC
* *
37872 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTT
37918 CAAAAGGATA
Statistics
Matches: 128, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
52 4 0.03
53 47 0.37
54 7 0.05
55 66 0.52
56 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTATAAGGC
Found at i:37915 original size:108 final size:110
Alignment explanation
Indices: 37716--37916 Score: 307
Period size: 108 Copynumber: 1.8 Consensus size: 110
37706 TTTAAGGATA
* * *
37716 CCATATAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGTAAGGAAATCATGTAAGA
1 CCATATAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTATAAGGCAAGGAAACCATGTAAGA
*
37781 CCATGTCAAGACATGACATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGACAATGATAAGTTACTATAAGGCAAAGGTC
* * *
37826 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-GTTTATAAGGCAAGGATACCATGTAAGA
1 CCATATAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTATAAGGCAAGGAAACCATGTAAGA
* *
37889 CCATGTCAAGACATGGCAATGGTAAGTT
66 CCATGTCAAGACATGACAATGATAAGTT
37917 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 49 0.60
109 7 0.09
110 26 0.32
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (110 bp):
CCATATAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTATAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGACAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:41853 original size:46 final size:46
Alignment explanation
Indices: 41786--41910 Score: 205
Period size: 46 Copynumber: 2.7 Consensus size: 46
41776 TGTAACCCGC
** * *
41786 CCATAAGCAAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
41832 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
41878 CCATAAGTGAACTCGGACTCAACTCAACGAGCT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCT
41911 TAGATGCCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:46051 original size:50 final size:49
Alignment explanation
Indices: 45929--46112 Score: 208
Period size: 50 Copynumber: 3.7 Consensus size: 49
45919 CTGGTACGCA
* *
45929 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAATTATCGA-TACACG
** *
45978 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACTCG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAATTATC-GATACACG
* * * * * *
46028 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-TTATC-GATACACG
* *
46079 TAGTAGCCTGCACTTAGTACTAAACATATGACCT
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT
46113 CACAATAGAT
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 32 0.28
50 43 0.38
51 38 0.34
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAATTATCGATACACG
Found at i:46111 original size:101 final size:99
Alignment explanation
Indices: 45929--46112 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 99
45919 CTGGTACGCA
* *
45929 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCAGTACACATAGTAGCCTGCACTTA
* *
45994 GTACTACACATGTGACCTAACCATCTGATACTCG
66 GTACTAAACATATGACCTAACCATCTGATACTCG
* * ** *
46028 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCAGTACACATAGTAGCCTGCACT
46093 TAGTACTAAACATATGACCT
64 TAGTACTAAACATATGACCT
46113 CACAATAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 29 0.39
100 3 0.04
101 42 0.57
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCAGTACACATAGTAGCCTGCACTTA
GTACTAAACATATGACCTAACCATCTGATACTCG
Done.