Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4017
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: 16365
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Found at i:3882 original size:18 final size:17
Alignment explanation
Indices: 3856--3889 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3846 CCATAATACG
3856 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
3874 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
3890 AAGCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:8370 original size:79 final size:80
Alignment explanation
Indices: 8272--8454 Score: 239
Period size: 79 Copynumber: 2.3 Consensus size: 80
8262 AACTCGTTCA
* *
8272 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
8335 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
**
8352 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
*
8416 ATAGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
8431 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
8455 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:8454 original size:40 final size:40
Alignment explanation
Indices: 8254--8454 Score: 248
Period size: 40 Copynumber: 5.0 Consensus size: 40
8244 AATTTAACCA
* ** *
8254 GATATAGCAACTCGTTCAAATGCCTTCGGGACATAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
8294 GTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
8334 GATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
8373 GA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 GATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCG
* *
8413 GATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 GATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
8453 GA
1 GA
8455 CATCATTCGA
Statistics
Matches: 139, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:10091 original size:1 final size:1
Alignment explanation
Indices: 10087--10195 Score: 218
Period size: 1 Copynumber: 109.0 Consensus size: 1
10077 TATGACTCGG
10087 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10152 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10196 ATGACTCGGT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 108 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14791 original size:40 final size:40
Alignment explanation
Indices: 14746--14926 Score: 203
Period size: 40 Copynumber: 4.5 Consensus size: 40
14736 GCATCGCTTC
*
14746 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
* *
14786 AATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACA
*
14826 AATGCCTTCGGG-CTTAG-CCGG-AATTAGTAACTCGGCACA
1 AATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTC-GCACA
* * * *
14865 AATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACA
14906 AA-GCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
14927 AACATCATTC
Statistics
Matches: 121, Mismatches: 10, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
38 15 0.12
39 17 0.14
40 65 0.54
41 22 0.18
42 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
Found at i:14870 original size:79 final size:79
Alignment explanation
Indices: 14745--14924 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 79
14735 AGCATCGCTT
* *
14745 CAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 CAATGCCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
14809 ATTTAGTAAC-TCGCA
64 ATATAGTAACTTAGCA
**
14824 CCAATGCCTTCGGG-CTTAGCCGGA-ATTAGTAACTCGGCACAAATGCCTTCGGATCTTAGTCCG
1 -CAATGCCTTCGGGACTTAGCCGGATA-TAGTAACTC-GCACAAATGCCTTCGGATCTTAACCCG
*
14887 GATATAGTCACTTAGCA
63 GATATAGTAACTTAGCA
*
14904 CAAAGCCTTCGGGACTTAGCC
1 CAATGCCTTCGGGACTTAGCC
14925 CGAACATCAT
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 16 0.18
79 46 0.53
80 24 0.28
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CAATGCCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCA
Done.