Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_106 ID=scaffold_106-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: 14323
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.27
Warning! 864 characters in sequence are not A, C, G, or T
Found at i:1367 original size:23 final size:23
Alignment explanation
Indices: 1337--1382 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1327 AGAAAGGTGA
1337 TAGTTTGGCCGAGGGGTATGTGT
1 TAGTTTGGCCGAGGGGTATGTGT
1360 TAGTTTGGCCGAGGGGTATGTGT
1 TAGTTTGGCCGAGGGGTATGTGT
1383 CAGAGTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.43, T:0.35
Consensus pattern (23 bp):
TAGTTTGGCCGAGGGGTATGTGT
Found at i:3360 original size:20 final size:20
Alignment explanation
Indices: 3335--3374 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3325 TTCACCTCAT
3335 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
3355 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
3375 AAGACCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:11566 original size:45 final size:45
Alignment explanation
Indices: 11501--11661 Score: 137
Period size: 44 Copynumber: 3.6 Consensus size: 45
11491 AGTAGATCAG
* * *
11501 AGATCAGAAAAAAGCTGATCTTGCCTTCCCATACTGGTGGCGAAGC
1 AGATCA-AAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGC
*** * * * *
11547 AGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
1 AGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGC
* * * *
11591 AGATCAAAGAAAG-AGATCTTGTCTCCCCATACTGGTGGTGGAGT
1 AGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGC
* * * *
11635 AGGTCGAAGAAAACAGATCGTGTCTTC
1 AGATCAAAGAAAGCAGATCTTGTCTTC
11662 ATGTACTGGC
Statistics
Matches: 91, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
43 17 0.19
44 34 0.37
45 34 0.37
46 6 0.07
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (45 bp):
AGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGC
Found at i:11666 original size:88 final size:88
Alignment explanation
Indices: 11517--11688 Score: 254
Period size: 88 Copynumber: 2.0 Consensus size: 88
11507 GAAAAAAGCT
* * * *
11517 GATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTG
1 GATCTTGCCTCCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCGTGTCTTCATGTACTG
11582 GCGTGAAGTAGATCAAAGAAAGA
66 GCGTGAAGTAGATCAAAGAAAGA
* * * * * *
11605 GATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAAACAGATCGTGTCTTCATGTACTG
1 GATCTTGCCTCCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCGTGTCTTCATGTACTG
11670 GCGTGAAGTAGATCAAAGA
66 GCGTGAAGTAGATCAAAGA
11689 TAGTAGGTCC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (88 bp):
GATCTTGCCTCCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCGTGTCTTCATGTACTG
GCGTGAAGTAGATCAAAGAAAGA
Found at i:11705 original size:44 final size:44
Alignment explanation
Indices: 11542--11688 Score: 170
Period size: 44 Copynumber: 3.3 Consensus size: 44
11532 TACTGGTGGC
* *
11542 GAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
* *** *
11586 GAAGTAGATCAAAGAAAG-AGATCTTGTCTCCCCATACTGGTGGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGT
* * * * *
11630 GGAGTAGGTCGAAGAAAACAGATCGTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
11674 GAAGTAGATCAAAGA
1 GAAGTAGATCAAAGA
11689 TAGTAGGTCC
Statistics
Matches: 81, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
43 17 0.21
44 47 0.58
45 17 0.21
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (44 bp):
GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
Found at i:11749 original size:88 final size:88
Alignment explanation
Indices: 11528--11731 Score: 221
Period size: 88 Copynumber: 2.3 Consensus size: 88
11518 ATCTTGCCTT
* * * * * * * *
11528 CCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
1 CCCATACTGGTAGCGAAGTAGGTCGAAGAAAACAGATCGTATCTTCATGTACTGGCGTGAAGTAG
*
11593 ATCAAAGAAAGAGATCTTGTCTC
66 ATCAAAGAAAGAGATCCTGTCTC
* * * *
11616 CCCATACTGGTGGTGGAGTAGGTCGAAGAAAACAGATCGTGTCTTCATGTACTGGCGTGAAGTAG
1 CCCATACTGGTAGCGAAGTAGGTCGAAGAAAACAGATCGTATCTTCATGTACTGGCGTGAAGTAG
* * *
11681 ATCAAAGATAGTAGGTCCTGTCTT
66 ATCAAAGAAAG-AGATCCTGTCTC
* *
11705 CCTATATTGGTAGCGAAGT-GGATCGAA
1 CCCATACTGGTAGCGAAGTAGG-TCGAA
11732 TATACATATT
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
88 69 0.71
89 28 0.29
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (88 bp):
CCCATACTGGTAGCGAAGTAGGTCGAAGAAAACAGATCGTATCTTCATGTACTGGCGTGAAGTAG
ATCAAAGAAAGAGATCCTGTCTC
Found at i:14008 original size:12 final size:12
Alignment explanation
Indices: 13991--14021 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13981 ACATGCATTT
13991 TATATATATACA
1 TATATATATACA
14003 TATATATATACA
1 TATATATATACA
*
14015 CATATAT
1 TATATAT
14022 CACATTCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:14010 original size:14 final size:14
Alignment explanation
Indices: 13991--14021 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13981 ACATGCATTT
*
13991 TATATATATACATA
1 TATATATACACATA
14005 TATATATACACATA
1 TATATATACACATA
14019 TAT
1 TAT
14022 CACATTCCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATATACACATA
Done.