Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold921
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: 21279
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Found at i:7194 original size:79 final size:81
Alignment explanation
Indices: 7085--7267 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
7075 TACTCGTTCA
* *
7085 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
7148 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
7165 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
7228 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
7244 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
7268 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:7267 original size:40 final size:40
Alignment explanation
Indices: 7064--7267 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
7054 CGGAATTTAA
** *
7064 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7104 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7144 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7183 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
7223 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
7263 CCGGA
1 CCGGA
7268 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:9233 original size:29 final size:29
Alignment explanation
Indices: 9188--9303 Score: 121
Period size: 29 Copynumber: 4.0 Consensus size: 29
9178 TACCTGTATC
* *
9188 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
9216 TGGCCCCTTTAGGCCCAAATCACCTGT-ATA
1 TGG-CCCATTAGGCCCAAATCACAT-TCATA
* *
9246 TGGCCCATTAGACCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
9275 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
9303 T
1 T
9304 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.22
29 44 0.60
30 12 0.16
31 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:9250 original size:58 final size:58
Alignment explanation
Indices: 9179--9290 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
9169 AAATTCACAT
* * *
9179 ACCTGTATCTGGCCCATTA-AGCCC-AATCATATTCATATGGCCCCTTTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGA-CCCAAATCACATTCATATGG-CCCGTTAGGCCCAAATC
*
9237 ACCTGTATATGGCCCATTAGACCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAGACCCAAATCACATTCATATGGCCCGTTAGGCCCA
9291 GTCACATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 33 0.69
59 15 0.31
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAGACCCAAATCACATTCATATGGCCCGTTAGGCCCAAATC
Found at i:12780 original size:27 final size:27
Alignment explanation
Indices: 12750--12927 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
12740 ATATTGAGCC
* * *
12750 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * * *
12777 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
12804 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
** * *
12832 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
12859 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
12886 CGCACACTTAGTGCAATATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
12913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12928 GTACAATTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:12889 original size:82 final size:81
Alignment explanation
Indices: 12771--12926 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
12761 TGCTATATAA
* * *
12771 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
12836 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
12853 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAATATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
12917 CACTTAGTGC
65 CACTTAGTGC
12927 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 19 0.29
82 46 0.71
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20821 original size:27 final size:27
Alignment explanation
Indices: 20791--20969 Score: 148
Period size: 27 Copynumber: 6.6 Consensus size: 27
20781 ATATTGAGTC
* *
20791 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
20818 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
20845 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
20873 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
20900 CGCACACTTAGT-C-AGCATCATTTCATTT
1 CGCACACTTAGTGCTA-CAT-A-ATCAACT
* *
20928 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
20955 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20970 GTACAATTTA
Statistics
Matches: 125, Mismatches: 20, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
26 4 0.03
27 74 0.59
28 42 0.34
29 4 0.03
30 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20884 original size:55 final size:54
Alignment explanation
Indices: 20791--20969 Score: 191
Period size: 55 Copynumber: 3.3 Consensus size: 54
20781 ATATTGAGTC
* * * *
20791 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
20845 CGCACACTTAGTGCTACATAGTCAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
* ** * *
20900 CGCACACTTAGT-C-AGCATCATTTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTA-CAT-A-ATCAACTCGCACACTTAGTGCCACATAGTCAAAT
20955 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20970 GTACAATTTA
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 25 0.24
55 73 0.71
56 4 0.04
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Done.