Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_147 ID=scaffold_147-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: 10754
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:374 original size:3 final size:3
Alignment explanation
Indices: 366--409 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
356 TTCTTAAATT
366 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
410 TCTATATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:466 original size:27 final size:26
Alignment explanation
Indices: 436--511 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
426 CATGCACTAT
*
436 TTTTATATAATATATATATGCATTTTC
1 TTTTATATAATATATATATGCA-TTGC
* * *
463 TTTTTTAT-ATAGTATACACGCATTGC
1 TTTTATATAATA-TATATATGCATTGC
**
489 TTCTTACGTAATATATATATGCA
1 TT-TTATATAATATATATATGCA
512 AAAAAATATT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
26 8 0.22
27 26 0.70
28 3 0.08
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (26 bp):
TTTTATATAATATATATATGCATTGC
Found at i:5266 original size:12 final size:12
Alignment explanation
Indices: 5251--5310 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
5241 ATTCAATAAA
*
5251 AAAATCAAAATC
1 AAAATCAAAAAC
5263 AAAATCAAAAAAC
1 AAAATC-AAAAAC
*
5276 AAAAT-AGAAAAA
1 AAAATCA-AAAAC
**
5288 AAAATCAAAGTC
1 AAAATCAAAAAC
*
5300 AAAAGCAAAAA
1 AAAATCAAAAA
5311 AAGAGAAATC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
11 1 0.03
12 25 0.68
13 11 0.30
ACGTcount: A:0.73, C:0.12, G:0.05, T:0.10
Consensus pattern (12 bp):
AAAATCAAAAAC
Found at i:6186 original size:7 final size:7
Alignment explanation
Indices: 6172--6205 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
6162 GAAATGGAGG
6172 ATGAAAA
1 ATGAAAA
*
6179 ACGAAAA
1 ATGAAAA
6186 ATG-AAA
1 ATGAAAA
6192 ATGAAAA
1 ATGAAAA
6199 ATGAAAA
1 ATGAAAA
6206 GTAATAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (7 bp):
ATGAAAA
Found at i:6197 original size:13 final size:13
Alignment explanation
Indices: 6176--6205 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6166 TGGAGGATGA
6176 AAAACGAAAAATG
1 AAAACGAAAAATG
*
6189 AAAATGAAAAATG
1 AAAACGAAAAATG
6202 AAAA
1 AAAA
6206 GTAATAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAACGAAAAATG
Found at i:7771 original size:44 final size:44
Alignment explanation
Indices: 7710--8136 Score: 245
Period size: 44 Copynumber: 9.8 Consensus size: 44
7700 AAGAGATTCA
7710 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * *
7754 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-TAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
** ** ** * * *
7797 AGATCTTATCTATCTGA-AGTTACAGCAGAGTGGATCGCA-TCAG-
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
* * * * * **
7840 -GTCTTATCTCCATGA-AGTTGCAGCGGAGCAGACTGAGTAAACAG-
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA--AGCCAGT
* * * * * ** *
7884 -GTCTTATCCCCCT-AAAGTTACAGTGGGGCAGATCGAAGAGATT
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
* * **
7927 CAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAGT
1 --AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * * *
7973 AATCCTATCTCCTTGAGATTACAGTGGAGC-GAATTAAAG-TAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAG-ATTGAAGCCAGT
* * ** * *
8016 AGATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATTGCA-TCA--
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
*
8058 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
*
8102 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
8137 AAAGTAATAG
Statistics
Matches: 287, Mismatches: 75, Indels: 42
0.71 0.19 0.10
Matches are distributed among these distances:
41 54 0.19
42 7 0.02
43 11 0.04
44 183 0.64
45 1 0.00
46 29 0.10
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
Found at i:7887 original size:219 final size:219
Alignment explanation
Indices: 7623--8090 Score: 735
Period size: 219 Copynumber: 2.1 Consensus size: 219
7613 GCCACCGACC
* * * * *
7623 CTTATCTCCCTAAAGTTGCAGCGGAGTAGACTGAGAAAGCAGGTCTTATTCCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAGCAGGTCTTATCCCCCTAAAGTTACAG
* * **
7688 TGGGGCAGATCGAAGAGATTCAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
66 TGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAG
7753 TAATCCTATCTCCCTGAGATTACAGTGGAGC-AGATTAAAGTAATAGATCTTATCTATCTGAAGT
131 TAATCCTATCTCCCTGAGATTACAGTGGAGCGA-ATTAAAGTAATAGATCTTATCTATCTGAAGT
**
7817 TACAGCAGAGTGGATCGCATCAGGT
195 TACAGCAGAGTGGATCGCATCAAAT
*
7842 CTTATCTCCATGAAGTTGCAGCGGAGCAGACTGAGTAAA-CAGGTCTTATCCCCCTAAAGTTACA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAG-AAAGCAGGTCTTATCCCCCTAAAGTTACA
7906 GTGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCA
65 GTGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCA
* *
7971 GTAATCCTATCTCCTTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGT
130 GTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTATCTGAAGT
* *
8036 TACAGTAGAGTGGATTGCATCAAAT
195 TACAGCAGAGTGGATCGCATCAAAT
*
8061 CTTATCTCCCTG-AGATTACAGCGGAGCAGA
1 CTTATCTCCCTGAAG-TTGCAGCGGAGCAGA
8091 TTGAAGCCAG
Statistics
Matches: 228, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
218 2 0.01
219 222 0.97
220 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (219 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAGCAGGTCTTATCCCCCTAAAGTTACAG
TGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAG
TAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTATCTGAAGTT
ACAGCAGAGTGGATCGCATCAAAT
Found at i:8086 original size:129 final size:129
Alignment explanation
Indices: 7926--8202 Score: 439
Period size: 129 Copynumber: 2.1 Consensus size: 129
7916 TCGAAGAGAT
* * *
7926 TCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
1 TCAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGA
* * **
7991 TTACAGTGGAGC-GAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
66 TTACAGTGGAGCAG-ATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGCAGAGTGGATCACA
*
8055 TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGA
1 TCAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGA
*
8120 TTACAGTGGAGCAGATTAAAGTAATAGATCTTATCTTTCTAAAGTTACAGCAGAGTGGATCACA
66 TTACAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGCAGAGTGGATCACA
* *
8184 TCAAGTCTTATCCCCCTGA
1 TCAAATCTTATCTCCCTGA
8203 AGTCACAGTG
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
129 135 0.99
130 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (129 bp):
TCAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGCAGAGTGGATCACA
Found at i:8308 original size:44 final size:43
Alignment explanation
Indices: 8185--8313 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 43
8175 TGGATCACAT
* * **
8185 CAAGTCTTATCCCCCTGAAGTCACAGTGGGACA-AATCGAAGATGA
1 CAAGTCTTATCCCCCTGAAGTTACAGTGGG-CAGACT-G-AGAAAA
* * * * * *
8230 CAAATCTTATCTCCTTGAGGTTGCAATGGAGCAGACTGAGAAAA
1 CAAGTCTTATCCCCCTGAAGTTACAGTGG-GCAGACTGAGAAAA
8274 CAAGTCTTATCCCCCTGAAGTTACAGTGAGGCAGACTGAG
1 CAAGTCTTATCCCCCTGAAGTTACAGTG-GGCAGACTGAG
8314 CATAGCAAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
44 36 0.55
45 26 0.40
46 3 0.05
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (43 bp):
CAAGTCTTATCCCCCTGAAGTTACAGTGGGCAGACTGAGAAAA
Found at i:9356 original size:6 final size:6
Alignment explanation
Indices: 9345--9397 Score: 90
Period size: 6 Copynumber: 8.8 Consensus size: 6
9335 TTAGTTTCGT
9345 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT- TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA
9393 TTTTT
1 TTTTT
9398 TTCGCTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 2 0.04
6 41 0.91
7 2 0.04
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:9963 original size:3 final size:3
Alignment explanation
Indices: 9955--9980 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9945 TTTTTAAATT
9955 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
9981 TCTATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10077 original size:2 final size:2
Alignment explanation
Indices: 10070--10101 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10060 TTCGTACGTA
10070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10102 GCAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.