Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1150
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: 39745
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:7154 original size:40 final size:40
Alignment explanation
Indices: 7099--7363 Score: 462
Period size: 40 Copynumber: 6.7 Consensus size: 40
7089 AACATTGGAT
7099 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
7139 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
7179 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
7219 CATATCCGGGCTAAGA-CCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
7258 TATATCCGGGCTATGA-CCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
7297 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
7337 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
7364 ATGTGTTTGC
Statistics
Matches: 214, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 73 0.34
40 141 0.66
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:7318 original size:79 final size:80
Alignment explanation
Indices: 7099--7363 Score: 462
Period size: 79 Copynumber: 3.3 Consensus size: 80
7089 AACATTGGAT
7099 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGC
7164 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
*
7179 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGA-CCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGC
7243 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
* * *
7258 TATATCCGGGCTATGA-CCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGC
7322 AATTATGCGAGTTGA
66 AATTATGCGAGTTGA
* *
7337 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
7364 ATGTGTTTGC
Statistics
Matches: 175, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
78 36 0.21
79 74 0.42
80 65 0.37
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (80 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGC
AATTATGCGAGTTGA
Found at i:13299 original size:37 final size:37
Alignment explanation
Indices: 13251--13358 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
13241 GCTCGGACGT
* * *
13251 AATCTCTACACGAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
13288 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
13325 AATCTCCACACGTAGTCATCGGGTCTCACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
13359 ATATATTTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
Found at i:13573 original size:47 final size:47
Alignment explanation
Indices: 13521--13753 Score: 349
Period size: 47 Copynumber: 5.0 Consensus size: 47
13511 TTTCACACTA
* * * * * *
13521 GCCATTCGGCTTTACCGCATATATGCATTTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
13568 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
13615 GCCATTCGGCCTTATCACATATATGCATGCTCACATTTATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
13662 GCCATTCGGCCTCATCACATATATGCATGTTCACATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
*
13709 GCCATTCGGCCTCATCACATATATGCATGTTCACATTCATCACAT
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
13754 AAAATCCTAA
Statistics
Matches: 171, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 171 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:13748 original size:25 final size:25
Alignment explanation
Indices: 13673--13754 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
13663 CCATTCGGCC
13673 TCATCACATATATGCATGTTCACAT
1 TCATCACATATATGCATGTTCACAT
* * * *
13698 TCACCACAT-T-GGCCA--TTCGGC-C
1 TCATCACATATATG-CATGTTC-ACAT
13720 TCATCACATATATGCATGTTCACAT
1 TCATCACATATATGCATGTTCACAT
13745 TCATCACATA
1 TCATCACATA
13755 AAATCCTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
22 11 0.26
23 5 0.12
24 5 0.12
25 21 0.50
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (25 bp):
TCATCACATATATGCATGTTCACAT
Found at i:33109 original size:27 final size:27
Alignment explanation
Indices: 33079--33256 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
33069 ATATTGAGTC
* * * *
33079 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
33106 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
33133 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
33161 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
33188 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
33215 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
33242 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
33257 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:33218 original size:82 final size:81
Alignment explanation
Indices: 33100--33255 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
33090 TGCTATATAA
* *
33100 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
33165 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
33182 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
33246 CACTTAGTGC
65 CACTTAGTGC
33256 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.