Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold302
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: 28268
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6246 original size:16 final size:16
Alignment explanation
Indices: 6225--6257 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6215 AACCATTAAC
6225 AAAATATACATGTTGG
1 AAAATATACATGTTGG
6241 AAAATATACATGTTGG
1 AAAATATACATGTTGG
6257 A
1 A
6258 TAAAACAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AAAATATACATGTTGG
Found at i:16234 original size:6 final size:6
Alignment explanation
Indices: 16223--16300 Score: 63
Period size: 6 Copynumber: 12.8 Consensus size: 6
16213 GGTTTGAGAA
* * *
16223 AAAAAG AAAAAG AAAAAG --GAAG AAGAAAG AGAGAG AAAACAG AAAGAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAA-AG -AA-AAAG
*
16273 AAAAAG AAAAAG AAAAA- AAAGAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
16301 ATAAAAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 3 0.05
5 4 0.07
6 36 0.63
7 8 0.14
8 4 0.07
9 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16266 original size:17 final size:14
Alignment explanation
Indices: 16219--16294 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 14
16209 CTAGGGTTTG
*
16219 AGAAAAAAAGAAAA
1 AGAAAGAAAGAAAA
* *
16233 AGAAA-AAGGAAGA
1 AGAAAGAAAGAAAA
16246 AGAAAGAGAGAGAAAA
1 AGAAAGA-A-AGAAAA
16262 CAGAAAGAAAGAAAA
1 -AGAAAGAAAGAAAA
16277 AG-AA-AAAGAAAA
1 AGAAAGAAAGAAAA
16289 A-AAAGA
1 AGAAAGA
16295 GAAAAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 11 0.21
13 14 0.27
14 8 0.15
15 7 0.13
16 5 0.10
17 7 0.13
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAGAAAA
Found at i:16271 original size:21 final size:20
Alignment explanation
Indices: 16245--16300 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
16235 AAAAAGGAAG
16245 AAGAAAGAGAGAGAAAACAGA
1 AAGAAAGAGAGAGAAAA-AGA
* *
16266 AAGAAAGAAAAAGAAAAAGA
1 AAGAAAGAGAGAGAAAAAGA
16286 AA-AAA-A-AGAGAAAAA
1 AAGAAAGAGAGAGAAAAA
16301 ATAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 1 0.03
19 3 0.09
20 5 0.16
21 15 0.47
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAGAAAGAGAGAGAAAAAGA
Found at i:16299 original size:11 final size:11
Alignment explanation
Indices: 16221--16301 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
16211 AGGGTTTGAG
*
16221 AAAAAAAGAAA
1 AAAAAAAGAGA
16232 AAGAAAAAG-GA
1 AA-AAAAAGAGA
*
16243 AGAAGAAAGAGA
1 A-AAAAAAGAGA
* * *
16255 GAGAAAACAG-
1 AAAAAAAGAGA
*
16265 AAAGAAAGA-A
1 AAAAAAAGAGA
16275 AAAGAAAA-AGA
1 AAA-AAAAGAGA
16286 AAAAAAAGAGA
1 AAAAAAAGAGA
16297 AAAAA
1 AAAAA
16302 TAAAAATATA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
10 13 0.25
11 30 0.58
12 9 0.17
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:16471 original size:19 final size:21
Alignment explanation
Indices: 16449--16488 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
16439 AGTCCTTAAC
*
16449 AGCATGCCAG-CA-CCCAGCA
1 AGCAGGCCAGACAGCCCAGCA
16468 AGCAGGCCAGACAGCCCAGCA
1 AGCAGGCCAGACAGCCCAGCA
16489 GTAGGCATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.33, C:0.40, G:0.25, T:0.03
Consensus pattern (21 bp):
AGCAGGCCAGACAGCCCAGCA
Found at i:16539 original size:13 final size:13
Alignment explanation
Indices: 16521--16545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16511 TGTCAGCAGA
16521 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
16534 AAAAGAAAAAAA
1 AAAAGAAAAAAA
16546 ACAACAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:22873 original size:17 final size:17
Alignment explanation
Indices: 22853--22886 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
22843 ATTATTAAGA
22853 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
22870 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
22887 TTAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:23106 original size:44 final size:45
Alignment explanation
Indices: 23043--23140 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
23033 CTATTACACC
*
23043 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCCTCTAT
* * **
23087 TCCATTACATTCAACCAAACAATTGATTTGTTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
23132 TCCATTACA
1 TCCATTACA
23141 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:24748 original size:54 final size:54
Alignment explanation
Indices: 24661--24768 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
24651 TTCGTCACTA
* * * *
24661 ATTTAAGATTGAAATCCCTGTTTCTAATCAAATTCGATTTAAGATTATTAAGTG
1 ATTTAAGATTAAAATACCTGTTTCTAATAAAATTCGATTTAAAATTATTAAGTG
* *
24715 ATTTAAGATTAAAATACCT-TTTTTAAATAAAATTTGATTTAAAATTATTAAGTG
1 ATTTAAGATTAAAATACCTGTTTCT-AATAAAATTCGATTTAAAATTATTAAGTG
24769 TATAAATCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (54 bp):
ATTTAAGATTAAAATACCTGTTTCTAATAAAATTCGATTTAAAATTATTAAGTG
Done.