Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3814
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: 29648
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Found at i:344 original size:22 final size:22
Alignment explanation
Indices: 317--388 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
307 GCTCACATTC
317 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
339 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
363 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
386 ATC
1 ATC
389 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:394 original size:47 final size:47
Alignment explanation
Indices: 260--413 Score: 236
Period size: 47 Copynumber: 3.3 Consensus size: 47
250 AACTTAAGCA
* * *
260 GTTCATATTCATCACATTGGCCATTCGGCCTTATCACACATACGCAT
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
*
307 GCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
* * *
354 GTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATACAC
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
*
401 ATTCACATTCATC
1 GTTCACATTCATC
414 GCATGAAATC
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 98 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (47 bp):
GTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
Found at i:4042 original size:39 final size:40
Alignment explanation
Indices: 3925--4109 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
3915 GCTACTCGTT
* *
3925 CAAATGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
3965 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
4005 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
4044 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
4085 CAAA-GCCTTCAGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4110 CATCATTCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 77 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:4093 original size:79 final size:80
Alignment explanation
Indices: 3953--4109 Score: 194
Period size: 79 Copynumber: 2.0 Consensus size: 80
3943 AGCCCGGTTA
* * *
3953 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTC-G
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCAG
*
4017 GGCTTAGCCCGGAAT
66 GACTTAGCCCGGAAT
* ** * *
4032 TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTC
4095 AGGACTTAGCCCGGA
64 AGGACTTAGCCCGGA
4110 CATCATTCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
78 3 0.05
79 46 0.70
80 17 0.26
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCAG
GACTTAGCCCGGAAT
Found at i:7382 original size:38 final size:38
Alignment explanation
Indices: 7340--7415 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
7330 CAAGAACTCC
7340 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
7378 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
7416 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:14936 original size:79 final size:81
Alignment explanation
Indices: 14827--15009 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
14817 TACTCGTTCA
* *
14827 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
14890 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
14907 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
14970 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
14986 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
15010 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:15009 original size:40 final size:40
Alignment explanation
Indices: 14806--15009 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
14796 CGGAATTTAA
** *
14806 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
14846 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
14886 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
14925 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
14965 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
15005 CCGGA
1 CCGGA
15010 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:18874 original size:40 final size:40
Alignment explanation
Indices: 18798--19189 Score: 649
Period size: 40 Copynumber: 9.8 Consensus size: 40
18788 CCAACATGAT
* * * * *
18798 TGCTCTTCGGGACCTAGCCCGGAGATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
18838 TGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
18878 TGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
**
18918 TGCTCTTCGACACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
18958 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
18998 TGCTCTTCGGGACTTAGCCCAGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
19038 TGCTCTTCGGGAATTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
19078 CGCTCTTCAGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
19118 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
19158 TGCTCTTCGGGACTTAGCCCGGGTATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
19190 CTCAATTCTC
Statistics
Matches: 331, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 331 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.22
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:20509 original size:37 final size:37
Alignment explanation
Indices: 20450--20557 Score: 148
Period size: 37 Copynumber: 3.0 Consensus size: 37
20440 AGCTCAGACG
* * * *
20450 AAATCTCCACACGAAGTTATCGGGTCTCAACCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
*
20487 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
*
20524 TAATCTCCACACGTAGTC--CGGGTCTTACCCGGAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAA
20558 TATTTCCAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
35 15 0.23
37 49 0.77
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
Found at i:20876 original size:50 final size:48
Alignment explanation
Indices: 20704--20851 Score: 287
Period size: 48 Copynumber: 3.1 Consensus size: 48
20694 CATCACCTAC
*
20704 ATATTTCACACTAGCCATTCGGCTTTACTACATATACATATCTCATAT
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
20752 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
20800 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
20848 ATAT
1 ATAT
20852 ATTTCACATT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 99 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT
Found at i:21025 original size:47 final size:47
Alignment explanation
Indices: 20855--21044 Score: 247
Period size: 47 Copynumber: 4.0 Consensus size: 47
20845 TATATATATT
* * * *
20855 TCACATTGACCGTTCGGCTTTATCAC-TCATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACAT-ATATGCATGTTCACATTCA
* * *
20902 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCG
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
20949 TCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * **
20996 TCACATTGGCCATTTGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
21043 TC
1 TC
21045 GCATGAAATC
Statistics
Matches: 125, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
47 125 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Done.