Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_151 ID=scaffold_151-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: 10721
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:5794 original size:8 final size:7
Alignment explanation
Indices: 5770--5806 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
5760 TTTGAGTAAA
5770 AAAAATG
1 AAAAATG
5777 -AAAATG
1 AAAAATG
5783 AAAAATG
1 AAAAATG
5790 AAAAATG
1 AAAAATG
5797 AAAAAATG
1 -AAAAATG
5805 AA
1 AA
5807 CAAGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 15 0.54
8 7 0.25
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:5794 original size:14 final size:15
Alignment explanation
Indices: 5769--5806 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
5759 CTTTGAGTAA
5769 AAAAAATG-AAAATG
1 AAAAAATGAAAAATG
5783 -AAAAATGAAAAATG
1 AAAAAATGAAAAATG
5797 AAAAAATGAA
1 AAAAAATGAA
5807 CAAGTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:5815 original size:15 final size:13
Alignment explanation
Indices: 5769--5816 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
5759 CTTTGAGTAA
5769 AAAAAATGAAAAT
1 AAAAAATGAAAAT
*
5782 GAAAAATGAAAAAT
1 AAAAAATG-AAAAT
5796 GAAAAAATGAACAAGT
1 -AAAAAATGAA-AA-T
5812 AAAAA
1 AAAAA
5817 TGGAGAGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 7 0.24
14 7 0.24
15 14 0.48
16 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAAAATGAAAAT
Found at i:7275 original size:45 final size:44
Alignment explanation
Indices: 7225--7364 Score: 124
Period size: 45 Copynumber: 3.2 Consensus size: 44
7215 GGAGCAGGTT
7225 AAAGATAGCAGATCTTGCATTCCTGCATCGACAGCGAAGCAGATC
1 AAAGATAGCAGATCTTGC-TTCCTGCATCGACAGCGAAGCAGATC
* * * * * * * * * *
7270 GAAGATACCAG-CCTTGCCTCCTTCGGT-TACAG-TAGAGCAGGTT
1 AAAGATAGCAGATCTTGCTTCCTGC-ATCGACAGCGA-AGCAGATC
*
7313 AAAGATAGCAGATCTTGCCTTCCTGTATCGACAGCGAAGCAGATC
1 AAAGATAGCAGATCTTG-CTTCCTGCATCGACAGCGAAGCAGATC
7358 AAAGATA
1 AAAGATA
7365 CAAGCCTTGC
Statistics
Matches: 68, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
42 1 0.01
43 24 0.35
44 11 0.16
45 31 0.46
46 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (44 bp):
AAAGATAGCAGATCTTGCTTCCTGCATCGACAGCGAAGCAGATC
Found at i:7318 original size:43 final size:43
Alignment explanation
Indices: 7183--7319 Score: 107
Period size: 43 Copynumber: 3.1 Consensus size: 43
7173 AAACAGATCG
* * *
7183 AAGATACCAGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTA
1 AAGATACCAGCCTTGCCTCCTTCGGTTACAGTAGAGCAGGTTA
* * * * * * * * **
7226 AAGATAGCAGATCTTGCATTCCTGC-ATCGACAG-CGAAGCAGATCG
1 AAGATACCAG-CCTTGC-CTCCTTCGGT-TACAGTAG-AGCAGGTTA
7271 AAGATACCAGCCTTGCCTCCTTCGGTTACAGTAGAGCAGGTTA
1 AAGATACCAGCCTTGCCTCCTTCGGTTACAGTAGAGCAGGTTA
7314 AAGATA
1 AAGATA
7320 GCAGATCTTG
Statistics
Matches: 66, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
43 30 0.45
44 14 0.21
45 22 0.33
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (43 bp):
AAGATACCAGCCTTGCCTCCTTCGGTTACAGTAGAGCAGGTTA
Found at i:7374 original size:44 final size:44
Alignment explanation
Indices: 7237--7552 Score: 136
Period size: 44 Copynumber: 7.2 Consensus size: 44
7227 AGATAGCAGA
* * *
7237 TCTTGCATTCCTGCATCGACAGCGAAGCAGATCGAAGATACCAG
1 TCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATACAAG
* * * **
7281 CCTTGCC-TCC--T-TCGGTTACAG-TAGAGCAGGTTAAAGATAGC-AG
1 TCTTGCCTTCCTGTATC-G--ACAGCGA-AGCAGATCGAAGATA-CAAG
*
7324 ATCTTGCCTTCCTGTATCGACAGCGAAGCAGATCAAAGATACAAG
1 -TCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATACAAG
* * * * * * ** * ** *
7369 CCTTGCCTCCCACAGT-T-G-TAGTGGATTAGGTTAAAGATAAAAG
1 TCTTGCCT-TC-CTGTATCGACAGCGAAGCAGATCGAAGATACAAG
*
7412 ATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAG
1 -TCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATACAAG
* * * * * * *
7457 TCTTGCCTCCCTCGGT-T-G-TAGTGGAGCAGGTTGAAGACAGC-AG
1 TCTTGCCTTCCT--GTATCGACAGCGAAGCAGATCGAAGATA-CAAG
* *
7500 ATCTTGCCTTCTTGTATCGACAGCGAAGCAGATCGAAGACACAAG
1 -TCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATACAAG
*
7545 CCTTGCCT
1 TCTTGCCT
7553 CCCTCGTTTG
Statistics
Matches: 195, Mismatches: 51, Indels: 52
0.65 0.17 0.17
Matches are distributed among these distances:
40 2 0.01
41 1 0.01
42 5 0.03
43 58 0.30
44 61 0.31
45 59 0.30
46 5 0.03
47 2 0.01
48 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (44 bp):
TCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATACAAG
Found at i:7578 original size:88 final size:88
Alignment explanation
Indices: 7051--7565 Score: 676
Period size: 88 Copynumber: 5.9 Consensus size: 88
7041 CAGATCAGTG
* * *
7051 AAGATAGCAGATCTTGCCTTCCTGCATCGACAACGAAGCAAATCGAA-A-ACAAAGTCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATAC-AAGCCTTGCCTC
* * *
7114 CATCGGTTACAGTGGAGCGGGTTA
65 CCTCGGTTGCAGTGGAGCAGGTTA
* * * * * *
7138 AAGACAACAGATCTTGCCTTCCTGTA-CTGACAACGAAACAGATCGAAGATACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATC-GACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTC
*
7202 CATCGGTTGCAGTGGAGCAGGTTA
65 CCTCGGTTGCAGTGGAGCAGGTTA
* *
7226 AAGATAGCAGATCTTGCATTCCTGCATCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCC
* * *
7291 TTCGGTTACAGTAGAGCAGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
* *
7314 AAGATAGCAGATCTTGCCTTCCTGTATCGACAGCGAAGCAGATCAAAGATACAAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCC
* * * **
7379 CACAGTTGTAGTGGATTAGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
** *
7402 AAGATAAAAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAGTCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCC
* *
7467 CTCGGTTGTAGTGGAGCAGGTTG
66 CTCGGTTGCAGTGGAGCAGGTTA
* * * *
7490 AAGACAGCAGATCTTGCCTTCTTGTATCGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCC
*
7555 CTCGTTTGCAG
66 CTCGGTTGCAG
7566 CGAAACAGGT
Statistics
Matches: 375, Mismatches: 49, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
86 1 0.00
87 40 0.11
88 331 0.88
89 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCC
CTCGGTTGCAGTGGAGCAGGTTA
Found at i:7832 original size:132 final size:128
Alignment explanation
Indices: 7614--8242 Score: 618
Period size: 128 Copynumber: 4.9 Consensus size: 128
7604 ACAGCGGAGT
* * * **
7614 ACATTGAAGCCAGTAA-TTCTATCTCCCTAGGT-AGTAGTGGAATATATT-GAAGATTACAGATC
1 ACATTGAAGCCA-CAAGTCCTATCTCCCT-GGTCAGCAGTGGAATAGGTTAGAA-ATTACAGATC
* * * * * * * * * * * *
7676 TTATCTCCCTCAGCAGTGGTGGAGCGGATCAAAGATGATGGATTTTACCTCCTTGAGGTTACAAT
63 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTTA--T-CTTCAAG--ACAAG
*
7741 GG-AGT
123 GGAAGC
** * *
7746 ACATTGAAGCCAGTAGTCCTATCTCCCTGATCAGCAGTGGAATAGGTTAGAAATTATAGATCTTG
1 ACATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTG
* **
7811 TCTCCCTAAGTAGTAGCGGAGCAGATCGAAGATGGTGAATCTTATCTTCAAGAGTAGGGAAGC
66 TCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTTATCTTCAAGACAAGGGAAGC
* * * *
7874 AGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATTGCAGATCTTG
1 ACATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTG
* * **
7939 TCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAGGGAAGC
66 TCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTTATCTTCAAGACAAGGGAAGC
* * * * *
8002 AGATTTAAGCCACAAGTCCTATCTCCCTGGTCAACATGTGGAATATGTTAGAAATTATAGATCTT
1 ACATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCA-GTGGAATAGGTTAGAAATTACAGATCTT
* * * * * * **
8067 GTCTCCCTAAGCAGCAGCGGAGCAAATCGAAGACGGCGAATCTTATATTCAGGAGTAGGGAAGC
65 GTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTTATCTTCAAGACAAGGGAAGC
* * * * * *
8131 AGATTTAAGCCACAAGTCCTATCTCTCTGGTCAGCAGTGGAATAGGTTAGGAATTACAAATCTTA
1 ACATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTG
* * ** * * *
8196 TCTCCCTAAGTAGTAGTGGAATAGATTGAAGATTGTGAATCCTATCT
66 TCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTTATCT
8243 CCCTGGTCAG
Statistics
Matches: 429, Mismatches: 63, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
127 4 0.01
128 213 0.50
129 123 0.29
130 1 0.00
131 3 0.01
132 82 0.19
133 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (128 bp):
ACATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTG
TCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTTATCTTCAAGACAAGGGAAGC
Found at i:8108 original size:129 final size:128
Alignment explanation
Indices: 7760--8211 Score: 724
Period size: 128 Copynumber: 3.5 Consensus size: 128
7750 TGAAGCCAGT
* * *
7760 AGTCCTATCTCCCTGATCAGCAGTGGAATAGGTTAGAAATTATAGATCTTGTCTCCCTAAGTAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGT
* *
7825 AGCGGAGCAGATCGAAGATGGTGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACA
66 AGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACA
* *
7888 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATTGCAGATCTTGTCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGT
7953 AGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACA
66 AGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACA
* * *
8016 AGTCCTATCTCCCTGGTCAACATGTGGAATATGTTAGAAATTATAGATCTTGTCTCCCTAAGCAG
1 AGTCCTATCTCCCTGGTCAGCA-GTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAG
* * * *
8081 CAGCGGAGCAAATCGAAGACGGCGAATCTTATATTCAGGAGTAGGGAAGCAGATTTAAGCCACA
65 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACA
* * * * *
8145 AGTCCTATCTCTCTGGTCAGCAGTGGAATAGGTTAGGAATTACAAATCTTATCTCCCTAAGTAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGT
8210 AG
66 AG
8212 TGGAATAGAT
Statistics
Matches: 298, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
128 180 0.60
129 118 0.40
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (128 bp):
AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGT
AGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACA
Done.