Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_115 ID=scaffold_115-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: 15935
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.21
Warning! 3404 characters in sequence are not A, C, G, or T
Found at i:195 original size:41 final size:41
Alignment explanation
Indices: 149--370 Score: 322
Period size: 41 Copynumber: 5.4 Consensus size: 41
139 AGATTCACTA
*
149 GCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCG
1 GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCG
* * *
190 ACACTTAGCCTGCTAGGCTTATAA-TCTGATTTAGATCACCG
1 GCACTTAGCCTGCTAGGCTTA-AAGCCTGATTCAGATCACCG
* * *
231 GCACTTAGCCTACTAGGCTTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCG
*
272 GCACTTAGCCTGCTAGGCTTATAA-CCTGATTTAGATCACCG
1 GCACTTAGCCTGCTAGGCTTA-AAGCCTGATTCAGATCACCG
* *
313 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCG
354 GCACTTAGCCTGCTAGG
1 GCACTTAGCCTGCTAGG
371 TTTTAAAACC
Statistics
Matches: 160, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
40 2 0.01
41 155 0.97
42 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (41 bp):
GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCG
Found at i:286 original size:82 final size:82
Alignment explanation
Indices: 149--370 Score: 390
Period size: 82 Copynumber: 2.7 Consensus size: 82
139 AGATTCACTA
* * * *
149 GCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAA
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAA
*
214 TCTGATTTAGATCACCG
66 CCTGATTTAGATCACCG
*
231 GCACTTAGCCTACTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAA
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAA
296 CCTGATTTAGATCACCG
66 CCTGATTTAGATCACCG
313 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
371 TTTTAAAACC
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 133 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (82 bp):
GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAA
CCTGATTTAGATCACCG
Found at i:361 original size:123 final size:123
Alignment explanation
Indices: 149--370 Score: 356
Period size: 123 Copynumber: 1.8 Consensus size: 123
139 AGATTCACTA
*
149 GCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAA
1 GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAA
* *
214 TCTGATTTAGATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCAGTTCACCG
66 CCTGATTCAGATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCAGTTCACCG
* *
272 GCACTTAGCCTGCTAGGCTTATAA-CCTGATTTAGATCACCGGCACTTAGCCTGCTAGGCTTATA
1 GCACTTAGCCTGCTAGGCTTA-AAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATA
* * *
336 GCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
65 ACCTGATTCAGATCACCGGCACTTAGCCTACTAGG
371 TTTTAAAACC
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
123 88 0.98
124 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (123 bp):
GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAA
CCTGATTCAGATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCAGTTCACCG
Found at i:7531 original size:15 final size:15
Alignment explanation
Indices: 7513--7564 Score: 104
Period size: 15 Copynumber: 3.5 Consensus size: 15
7503 ATACGCAACC
7513 GGGATATCCCTCCTA
1 GGGATATCCCTCCTA
7528 GGGATATCCCTCCTA
1 GGGATATCCCTCCTA
7543 GGGATATCCCTCCTA
1 GGGATATCCCTCCTA
7558 GGGATAT
1 GGGATAT
7565 ACCTAAACCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (15 bp):
GGGATATCCCTCCTA
Found at i:7534 original size:30 final size:29
Alignment explanation
Indices: 7498--7581 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 29
7488 TCCTTGGATT
7498 GGGATATACGCAACCGGGATATCCCTCCTA
1 GGGATATAC-CAACCGGGATATCCCTCCTA
**
7528 GGGATAT-CCCTCCTAGGGATATCCCTCCTA
1 GGGATATACCAACC--GGGATATCCCTCCTA
7558 GGGATATACCTAAACCGGGATATC
1 GGGATATACC--AACCGGGATATC
7582 TGTAGAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
28 3 0.07
29 1 0.02
30 29 0.64
31 10 0.22
33 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (29 bp):
GGGATATACCAACCGGGATATCCCTCCTA
Found at i:7664 original size:21 final size:22
Alignment explanation
Indices: 7635--7676 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
7625 CCCGGTCCGG
*
7635 ACGCATAAAAAATCTGAACCGT
1 ACGCATAAAAAAACTGAACCGT
7657 ACGC-TAAAAAAACTGAACCG
1 ACGCATAAAAAAACTGAACCG
7677 GGCAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (22 bp):
ACGCATAAAAAAACTGAACCGT
Found at i:8135 original size:31 final size:32
Alignment explanation
Indices: 8086--8154 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
8076 GAAGGGGATA
*
8086 CCCCGAAAGAGCTTATACCGGACAGGGATATC
1 CCCCGAAAGAACTTATACCGGACAGGGATATC
8118 CCCCGAAA-AACTTATACCGGACAGGGATATC
1 CCCCGAAAGAACTTATACCGGACAGGGATATC
8149 CCCCGA
1 CCCCGA
8155 TATTCGTCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 28 0.78
32 8 0.22
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.14
Consensus pattern (32 bp):
CCCCGAAAGAACTTATACCGGACAGGGATATC
Found at i:15587 original size:15 final size:15
Alignment explanation
Indices: 15567--15597 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15557 GTGATTACGA
15567 TTGACTCCAAGCAAT
1 TTGACTCCAAGCAAT
15582 TTGACTCCAAGCAAT
1 TTGACTCCAAGCAAT
15597 T
1 T
15598 CAATTCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (15 bp):
TTGACTCCAAGCAAT
Done.