Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_120 ID=scaffold_120-JGI_221_v2.0
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: 12476
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.32
Warning! 215 characters in sequence are not A, C, G, or T
Found at i:3747 original size:50 final size:49
Alignment explanation
Indices: 3693--3833 Score: 120
Period size: 51 Copynumber: 2.8 Consensus size: 49
3683 TGTGATGTTG
* * *
3693 GGGAAGCAAGATTCACCATCGTGGCTTTAATCTGTTCCATTCCACCACCC
1 GGGAAGCAAGATTCACCAT-GTGGCTTTAATCTGTTCCACTACAACACCC
** * * * * * *** *
3743 GGGAAATAAAATTCACTATTGTAGCTTTAATCATTTTCAACTACAATGTCG
1 GGGAAGCAAGATTCACCA-TGTGGCTTTAATC-TGTTCCACTACAACACCC
3794 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
1 GGGAAGCAAGATTCACC-ATGTGGCTTTAATCTGTTCCAC
3834 CGCATCACCT
Statistics
Matches: 67, Mismatches: 21, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
50 31 0.46
51 35 0.52
52 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (49 bp):
GGGAAGCAAGATTCACCATGTGGCTTTAATCTGTTCCACTACAACACCC
Found at i:3920 original size:49 final size:49
Alignment explanation
Indices: 3766--4121 Score: 259
Period size: 50 Copynumber: 7.2 Consensus size: 49
3756 CACTATTGTA
* *
3766 GCTTTAATCATTTTCAACTACAATGTCGGGGAAGCAAGATTCACCGATGTG
1 GCTTTAATC-TTTTTAACTGCAATGTCGGGG-AGCAAGATTCACCGATGTG
* ** * ** * * * * * *
3817 GCTTTAATCTGTTCCACCGC-ATCACCTGAGGAGTAAGATTCGCTGTTGTA
1 GCTTTAATCTTTTTAACTGCAAT-GTC-GGGGAGCAAGATTCACCGATGTG
** *
3867 GCTTTAATCTTTTTAACTGCAATGTCAAGCAGCAAGATTCACCGATGTG
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCACCGATGTG
* ** * * * * * *
3916 GCTTTAATCTGTTCCACCGC-ATCGCCTGGGGAGTAAGATTCGCCGTTGTA
1 GCTTTAATCTTTTTAACTGCAAT-GTC-GGGGAGCAAGATTCACCGATGTG
** *
3966 GCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCAATGATATG
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCACCGATGTG
* * ** * * * * * * *
4015 GCATTAATCTATTCCACCGC-ATCGCCTGGGGAGTAAGATTCGCTGTTGTA
1 GCTTTAATCTTTTTAACTGCAAT-GTC-GGGGAGCAAGATTCACCGATGTG
4065 GCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCACCGATGTG
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCACCGATGTG
4114 GCTTTAAT
1 GCTTTAAT
4122 ACGTTCCACT
Statistics
Matches: 224, Mismatches: 72, Indels: 20
0.71 0.23 0.06
Matches are distributed among these distances:
48 4 0.02
49 95 0.42
50 107 0.48
51 18 0.08
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (49 bp):
GCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCACCGATGTG
Found at i:3929 original size:99 final size:99
Alignment explanation
Indices: 3616--4230 Score: 723
Period size: 99 Copynumber: 6.2 Consensus size: 99
3606 CGCCATTGCA
* ** * * * * * **
3616 GCTTTAATCCGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGCTTA
1 GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
** *
3681 ACTGTGATGTTGGGGAAGCAAGATTCACC-ATCGTG
66 ACTGCAATG-TCGGGAAGCAAGATTCACCGAT-GTG
* * * * * * * * *
3716 GCTTTAATCTGTTCCATTC-CACCACCCGGGAAATAAAATTCACTATTGTAGCTTTAATCATTTT
1 GCTTTAATCTGTTCCA-CCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATC-TTTT
* *
3780 CAACTACAATGTCGGGGAAGCAAGATTCACCGATGTG
64 TAACTGCAATGTC-GGGAAGCAAGATTCACCGATGTG
* *
3817 GCTTTAATCTGTTCCACCGCATCACCTGAGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
** *
3882 ACTGCAATGTCAAGCAGCAAGATTCACCGATGTG
66 ACTGCAATGTCGGGAAGCAAGATTCACCGATGTG
*
3916 GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
* ** *
3981 ACTGCAATGTCGGGGAGCAAGATTCAATGATATG
66 ACTGCAATGTCGGGAAGCAAGATTCACCGATGTG
* *
4015 GCATTAATCTATTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
*
4080 ACTGCAATGTCGGGGAGCAAGATTCACCGATGTG
66 ACTGCAATGTCGGGAAGCAAGATTCACCGATGTG
** *
4114 GCTTTAATAC-GTTCCACTACATCGCCTGGGGAGTAAGATTCGCTGTTGTAGTTTTAATCTTTTT
1 GCTTTAAT-CTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTT
* * * * *
4178 AACTACAATGTTGGGGAAGTAAGGTTCACCGTTGTG
65 AACTGCAATG-TCGGGAAGCAAGATTCACCGATGTG
* *
4214 GCATTAACCTGTTCCAC
1 GCTTTAATCTGTTCCAC
4231 TGTACCGCCA
Statistics
Matches: 447, Mismatches: 60, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
99 270 0.60
100 98 0.22
101 77 0.17
102 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (99 bp):
GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
ACTGCAATGTCGGGAAGCAAGATTCACCGATGTG
Found at i:4184 original size:50 final size:50
Alignment explanation
Indices: 3817--4181 Score: 258
Period size: 50 Copynumber: 7.4 Consensus size: 50
3807 CACCGATGTG
* ** * * *
3817 GCTTTAATCTGTTCCACCGCATCACCTGAGGAGTAAGATTCGCTGTTGTA
1 GCTTTAATCTTTTTAACTGCATCGCCTGGGGAGTAAGATTCGCTGTTGTA
* ** * * * * * *
3867 GCTTTAATCTTTTTAACTGCAAT-GTC-AAGCAGCAAGATTCACCGATGTG
1 GCTTTAATCTTTTTAACTGC-ATCGCCTGGGGAGTAAGATTCGCTGTTGTA
* ** * *
3916 GCTTTAATCTGTTCCACCGCATCGCCTGGGGAGTAAGATTCGCCGTTGTA
1 GCTTTAATCTTTTTAACTGCATCGCCTGGGGAGTAAGATTCGCTGTTGTA
* * ** * * *
3966 GCTTTAATCTTTTTAACTGCAAT-GTC-GGGGAGCAAGATTCAATGATATG
1 GCTTTAATCTTTTTAACTGC-ATCGCCTGGGGAGTAAGATTCGCTGTTGTA
* * ** *
4015 GCATTAATCTATTCCACCGCATCGCCTGGGGAGTAAGATTCGCTGTTGTA
1 GCTTTAATCTTTTTAACTGCATCGCCTGGGGAGTAAGATTCGCTGTTGTA
* * * * * *
4065 GCTTTAATCTTTTTAACTGCAAT-GTC-GGGGAGCAAGATTCACCGATGTG
1 GCTTTAATCTTTTTAACTGC-ATCGCCTGGGGAGTAAGATTCGCTGTTGTA
* ** *
4114 GCTTTAATAC-GTTCCACTACATCGCCTGGGGAGTAAGATTCGCTGTTGTA
1 GCTTTAAT-CTTTTTAACTGCATCGCCTGGGGAGTAAGATTCGCTGTTGTA
*
4164 GTTTTAATCTTTTTAACT
1 GCTTTAATCTTTTTAACT
4182 ACAATGTTGG
Statistics
Matches: 230, Mismatches: 74, Indels: 22
0.71 0.23 0.07
Matches are distributed among these distances:
48 6 0.03
49 102 0.44
50 116 0.50
51 6 0.03
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (50 bp):
GCTTTAATCTTTTTAACTGCATCGCCTGGGGAGTAAGATTCGCTGTTGTA
Found at i:4212 original size:50 final size:49
Alignment explanation
Indices: 3761--4212 Score: 221
Period size: 50 Copynumber: 9.1 Consensus size: 49
3751 AAATTCACTA
* * *
3761 TTGTAGCTTTAATCATTTTCAACTACAATGTCGGGGAAGCAAGATTCACCG
1 TTGTAGCTTTAATC-TTTTTAACTACAATGTTGGGG-AGTAAGATTCACCG
* * * ** ** ** * * *
3812 ATGTGGCTTTAATCTGTTCCACCGC-ATCACCTGAGGAGTAAGATTCGCTG
1 TTGTAGCTTTAATCTTTTTAACTACAAT--GTTGGGGAGTAAGATTCACCG
* *** * *
3862 TTGTAGCTTTAATCTTTTTAACTGCAATGTCAAGCAGCAAGATTCACCG
1 TTGTAGCTTTAATCTTTTTAACTACAATGTTGGGGAGTAAGATTCACCG
* * * ** ** * *
3911 ATGTGGCTTTAATCTGTTCCACCGC-ATCGCCTGGGGAGTAAGATTCGCCG
1 TTGTAGCTTTAATCTTTTTAACTACAAT-G-TTGGGGAGTAAGATTCACCG
* * * **
3961 TTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCAATG
1 TTGTAGCTTTAATCTTTTTAACTACAATGTTGGGGAGTAAGATTCACCG
* * * * * ** ** * * *
4010 ATATGGCATTAATCTATTCCACCGC-ATCGCCTGGGGAGTAAGATTCGCTG
1 TTGTAGCTTTAATCTTTTTAACTACAAT-G-TTGGGGAGTAAGATTCACCG
* * *
4060 TTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAGCAAGATTCACCG
1 TTGTAGCTTTAATCTTTTTAACTACAATGTTGGGGAGTAAGATTCACCG
* * * ** * * *
4109 ATGTGGCTTTAATAC-GTTCCACTAC-ATCGCCTGGGGAGTAAGATTCGCTG
1 TTGTAGCTTTAAT-CTTTTTAACTACAAT-G-TTGGGGAGTAAGATTCACCG
* *
4159 TTGTAGTTTTAATCTTTTTAACTACAATGTTGGGGAAGTAAGGTTCACCG
1 TTGTAGCTTTAATCTTTTTAACTACAATGTTGGGG-AGTAAGATTCACCG
4209 TTGT
1 TTGT
4213 GGCATTAACC
Statistics
Matches: 287, Mismatches: 99, Indels: 31
0.69 0.24 0.07
Matches are distributed among these distances:
48 6 0.02
49 106 0.37
50 152 0.53
51 23 0.08
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (49 bp):
TTGTAGCTTTAATCTTTTTAACTACAATGTTGGGGAGTAAGATTCACCG
Found at i:6739 original size:28 final size:28
Alignment explanation
Indices: 6708--6764 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
6698 TCCTTTTTCC
6708 TTCTCTCTT-TTCATTTTT-ATTTTGATTT
1 TTCT-TCTTCTTC-TTTTTGATTTTGATTT
*
6736 TTCTTTTTCTTCTTTTTGATTTTGATTT
1 TTCTTCTTCTTCTTTTTGATTTTGATTT
6764 T
1 T
6765 GATTTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74
Consensus pattern (28 bp):
TTCTTCTTCTTCTTTTTGATTTTGATTT
Found at i:6742 original size:18 final size:18
Alignment explanation
Indices: 6715--6794 Score: 67
Period size: 18 Copynumber: 4.6 Consensus size: 18
6705 TCCTTCTCTC
*
6715 TTTTCATTTTTATTTTGA
1 TTTTTATTTTTATTTTGA
* * *
6733 TTTTTCTTTTTCTTCT--
1 TTTTTATTTTTATTTTGA
* *
6749 TTTTGATTTTGATTTTGA
1 TTTTTATTTTTATTTTGA
* *
6767 TTTTGATTTTGATTTTGA
1 TTTTTATTTTTATTTTGA
6785 TTTTT-TTTTT
1 TTTTTATTTTT
6795 TGAATTGGAT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
16 11 0.22
17 4 0.08
18 34 0.69
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (18 bp):
TTTTTATTTTTATTTTGA
Found at i:6758 original size:6 final size:6
Alignment explanation
Indices: 6749--6788 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
6739 TTTTTCTTCT
6749 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
6789 TTTTTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:6794 original size:12 final size:12
Alignment explanation
Indices: 6715--6788 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
6705 TCCTTCTCTC
*
6715 TTTTCATTTTTA
1 TTTTGATTTTTA
*
6727 TTTTGATTTTTC
1 TTTTGATTTTTA
*
6739 TTTT--TCTTCT-
1 TTTTGAT-TTTTA
*
6749 TTTTGATTTTGA
1 TTTTGATTTTTA
*
6761 TTTTGATTTTGA
1 TTTTGATTTTTA
*
6773 TTTTGATTTTGA
1 TTTTGATTTTTA
6785 TTTT
1 TTTT
6789 TTTTTTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 5 0.09
11 5 0.09
12 43 0.81
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.73
Consensus pattern (12 bp):
TTTTGATTTTTA
Done.