Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1167
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: 36903
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Found at i:7107 original size:39 final size:39
Alignment explanation
Indices: 7006--7182 Score: 205
Period size: 39 Copynumber: 4.5 Consensus size: 39
6996 ATATCCGGAC
7006 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGT
* *
7046 TAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
7086 TAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * * *
7125 TAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
7164 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
7183 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 68 0.57
40 49 0.41
41 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:7122 original size:79 final size:78
Alignment explanation
Indices: 7000--7180 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 78
6990 GTGAATATAT
* * *
7000 CCGGACTAAGATCCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTG
1 CCGGGCTAAG-TCCGAAGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTG
*
7065 TGCGAGATACTAAAT
64 TGCGAGATACTAAAA
* * * *
7080 CCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAA-TCCGGGTTAAGTCCCGAAGGCATTGT
1 CCGGGCTAAGTCCGAAGGCATTCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGT
* *
7144 GTGAGTTACTAAAA
65 GCGAGATACTAAAA
*
7158 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGT-CCGAAGGCATT
7181 TGAACGAGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
78 25 0.29
79 51 0.59
80 11 0.13
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGGGCTAAGTCCGAAGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTG
CGAGATACTAAAA
Found at i:7200 original size:79 final size:79
Alignment explanation
Indices: 7000--7215 Score: 190
Period size: 79 Copynumber: 2.7 Consensus size: 79
6990 GTGAATATAT
* * ** * *
7000 CCGGACTAAGATCCGAAGGCATTTGTGCGAGAT-AC-AAATTCCGGGTTAAGCCCCGAAGGCCTT
1 CCGGGCTAAG-TCCGAAGGCATTCGAACGAG-TGACTAAA-TCCGGGTTAAGTCCCGAAGGCCAT
*
7063 TGTGCGAGATACTAAAT
63 TGTGCGAGATACTAAAA
* ** * *
7080 CCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG-CATTGT
1 CCGGGCTAAGTCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTGT
* *
7144 GTGAGTTACTAAAA
66 GCGAGATACTAAAA
* * * *
7158 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGT-CCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
7216 TACGTGATTT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 42 0.37
79 61 0.54
80 11 0.10
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTGT
GCGAGATACTAAAA
Found at i:14082 original size:29 final size:29
Alignment explanation
Indices: 14012--14131 Score: 120
Period size: 29 Copynumber: 4.2 Consensus size: 29
14002 GAAAGCTTGT
* * * *
14012 ATATGAATGTGATGTGGGCCTAATGGGCT
1 ATATGAATATGATTTAGGCCTAATGGGCC
*
14041 GTATGAA-AGTGATTTAGGCCTAATGGGCC
1 ATATGAATA-TGATTTAGGCCTAATGGGCC
* *
14070 ATACGAATATGATTTAGTCCTAATGGGCC
1 ATATGAATATGATTTAGGCCTAATGGGCC
* *
14099 ATATGAATGA-GA-TTGGGCCTAGTGGGCC
1 ATATGAAT-ATGATTTAGGCCTAATGGGCC
14127 ATATG
1 ATATG
14132 CATGCATGTA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
28 18 0.24
29 56 0.74
30 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATGAATATGATTTAGGCCTAATGGGCC
Found at i:18702 original size:28 final size:29
Alignment explanation
Indices: 18619--18708 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 29
18609 TGTAGGCCCG
*
18619 TATGAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
* *
18648 TACGAAT-ATGATTTGGGCCTAACGGGCCA
1 TATGAATGA-GATTTGGGCCTAATGGGCCA
* *
18677 TATGAATGAGA-TTGGGTCTAGTGGGCCA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
18705 TATG
1 TATG
18709 CATGTATGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 18 0.35
29 33 0.63
30 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (29 bp):
TATGAATGAGATTTGGGCCTAATGGGCCA
Found at i:25965 original size:39 final size:39
Alignment explanation
Indices: 25870--26049 Score: 177
Period size: 40 Copynumber: 4.5 Consensus size: 39
25860 TGATGTCCGC
* * *
25870 GCTAAGTCCCGAAGGC-TTTGTGCCAAGTGACCATATTCGG
1 GCTAAGTCCCGAAGGCATTTGTG-CGAGTTACTA-ATTCGG
* *
25910 ACTAAGAT-CCGAAGGCATTTGTGCGACTTACTAATTCCGG
1 GCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATT-CGG
*
25950 GCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATTCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AATTCGG
* **
25989 GTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCGG
* * *
26029 GCTATGTCACGAAGGTATTTG
1 GCTAAGTCCCGAAGGCATTTG
26050 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 16, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
39 34 0.29
40 76 0.65
41 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCGG
Found at i:26071 original size:79 final size:79
Alignment explanation
Indices: 25918--26082 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 79
25908 GGACTAAGAT
* * **
25918 CCGAAGGCATTTGTGCGACTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGACTTACTAATACCGGGCTAAGCACGAAGGCATTGGAACGAGTTACTAA
* *
25983 ATTCGGGTTAAGTC
66 ATTCCGGTTAAATC
* * * *
25997 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCACGAAGGTATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGACTTACTAAT-ACCGGGCTAAG-CACGAAGGCATTGGAACGAGTTA-C
* *
26060 TATA-TCCGGTTAAATT
63 TAAATTCCGGTTAAATC
26076 CCGAAGG
1 CCGAAGG
26083 TACGTGATTC
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
78 2 0.03
79 50 0.70
80 19 0.27
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGACTTACTAATACCGGGCTAAGCACGAAGGCATTGGAACGAGTTACTAA
ATTCCGGTTAAATC
Found at i:34043 original size:40 final size:39
Alignment explanation
Indices: 33858--34036 Score: 195
Period size: 40 Copynumber: 4.5 Consensus size: 39
33848 TGAATGTTCC
* * * *
33858 GCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AACCGG
* *
33898 ACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCC-G
1 GCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-ACCGG
*
33937 GCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA-CCGG
*
33976 GTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AACCGG
*
34016 GCTATGTCCCGAAGGCATTTG
1 GCTAAGTCCCGAAGGCATTTG
34037 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
38 27 0.22
39 13 0.11
40 70 0.58
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAACCGG
Found at i:34068 original size:78 final size:78
Alignment explanation
Indices: 33906--34061 Score: 192
Period size: 78 Copynumber: 2.0 Consensus size: 78
33896 GGACTAAGAT
* **
33906 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
*
33971 TCCGGGTTAAGTC
66 TCCGGGTTAAATC
* *
33984 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACC-GGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
34047 TATATCC-GGTTAAAT
62 TAAATCCGGGTTAAAT
34062 TCGAAGGTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
77 2 0.03
78 26 0.39
79 15 0.22
80 24 0.36
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
TCCGGGTTAAATC
Done.