Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2017
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: 54314
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:4816 original size:27 final size:27
Alignment explanation
Indices: 4786--4962 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
4776 ATATTGAGTC
* * *
4786 CGCACACTCAATGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
4813 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
4839 CGCACACTTAGTGCTACATAATCAATCT
1 CGCACACTTAGTGCTACATAATCAA-CT
* ** *
4867 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
4894 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
4921 CGCACACTTAGTGC-ATCATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACT
*
4948 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
4963 GTACAATTTA
Statistics
Matches: 130, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
26 26 0.20
27 81 0.62
28 23 0.18
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:4892 original size:54 final size:54
Alignment explanation
Indices: 4786--4962 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 54
4776 ATATTGAGTC
* * * * * *
4786 CGCACACTCAATGCTATATAATCAA-CTCGCACACTTAGTGCTACGTAATCAAT
1 CGCACACTTAGTGCTACATAATCAATCTCGCACACTTAGTGCCACATAGTCAAT
*
4839 CGCACACTTAGTGCTACATAATCAATCTCGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAATCTCGCACACTTAGTGCCACATAGTCAA-T
* *
4894 CGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTG-CATCATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAATCTCGCACACTTAGTGCCA-CATAGTC-AAT
*
4948 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
4963 GTACAATTTA
Statistics
Matches: 107, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
53 24 0.22
54 60 0.56
55 23 0.21
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAATCTCGCACACTTAGTGCCACATAGTCAAT
Found at i:4903 original size:81 final size:81
Alignment explanation
Indices: 4807--4961 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
4797 TGCTATATAA
* * *
4807 TCAACTCGCACACTTAGTGC-TACGTAATCA-ATCGCACACTTAGTGC-TACATAATCAATCTCG
1 TCAACTCGCACACTTAGTGCAT-CATAATCATATCGCACACTTAGTGCAT-CATAATCAA-ATCA
4869 CACACTTAGTGCCACATGG
63 CACACTTAGTGCCACATGG
* * * *
4888 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCATCATAGTCAAATCACAC
1 TCAACTCGCACACTTAGTGCATCATAATCATATCGCACACTTAGTGCATCATAATCAAATCACAC
4953 ACTTAGTGC
66 ACTTAGTGC
4962 TGTACAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
81 39 0.61
82 24 0.38
83 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCATATCGCACACTTAGTGCATCATAATCAAATCACAC
ACTTAGTGCCACATGG
Found at i:8213 original size:93 final size:93
Alignment explanation
Indices: 8049--8220 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
8039 CGCCCATAAG
* *
8049 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
8114 ATGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
8142 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
8207 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
8221 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:8217 original size:46 final size:46
Alignment explanation
Indices: 8042--8217 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
8032 TGTAACCCGC
* *
8042 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * *
8088 CCATAGGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
8138 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
8181 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
8218 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.58
47 28 0.26
48 1 0.01
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:8236 original size:46 final size:45
Alignment explanation
Indices: 8050--8236 Score: 134
Period size: 46 Copynumber: 4.0 Consensus size: 45
8040 GCCCATAAGC
* * * *
8050 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA--TAGGT
1 GAACTCGGACTCAACTCAACGAGTTC-GG-ATGCTCAACCATCTA-GT
* * *
8096 GAACTCGGACTCAACTCAATGAGTTCGGATGC-CTAGTTA-CATTTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AGT
* * * *
8143 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCTAGT
8189 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAGT
8235 GA
1 GA
8237 CATGTCACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
43 1 0.01
44 13 0.12
45 3 0.03
46 59 0.52
47 30 0.27
48 1 0.01
49 5 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAGT
Found at i:29473 original size:51 final size:51
Alignment explanation
Indices: 29352--29527 Score: 174
Period size: 51 Copynumber: 3.5 Consensus size: 51
29342 CATGTGCGTA
* * * * * * * *
29352 GTACTAAGTGCAGGCTACTACGTGTACCGGAT-GATTAGGTCGCATGTGTA
1 GTACTAAGTACAGGCCACTATGTGTACCAGATAGCTTTGGTCACATGTGTG
* * * * *
29402 GTACTAAGTGCAAGCTACTATGTGTACCCGATAGCTTTGATCACATGTGTG
1 GTACTAAGTACAGGCCACTATGTGTACCAGATAGCTTTGGTCACATGTGTG
** *
29453 GTACTAAGTACAGGCCACTATGTGTAAAAGATAGCTTTGGTCACAAGTGTG
1 GTACTAAGTACAGGCCACTATGTGTACCAGATAGCTTTGGTCACATGTGTG
* * *
29504 GTACTATGTAAAGGCCACTTTGTG
1 GTACTAAGTACAGGCCACTATGTG
29528 AAGAAGGTAG
Statistics
Matches: 106, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 29 0.27
51 77 0.73
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (51 bp):
GTACTAAGTACAGGCCACTATGTGTACCAGATAGCTTTGGTCACATGTGTG
Found at i:29539 original size:51 final size:51
Alignment explanation
Indices: 29431--29572 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 51
29421 ATGTGTACCC
* * *
29431 GATAGCTTTGATCACATGTGTGGTACTAAGTACAGGCCACTATGTGTAAAA
1 GATAGCTTTGGTCACAAGTGTGGTACTATGTACAGGCCACTATGTGTAAAA
* *
29482 GATAGCTTTGGTCACAAGTGTGGTACTATGTAAAGGCCACTTTGTG-AAGAA
1 GATAGCTTTGGTCACAAGTGTGGTACTATGTACAGGCCACTATGTGTAA-AA
* * * *
29533 GGTAGCTTT-GACTACAAGGGTGGTACTATGTGCAGGCCAC
1 GATAGCTTTGGTC-ACAAGTGTGGTACTATGTACAGGCCAC
29573 CGGGCATCCG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
50 4 0.05
51 75 0.95
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GATAGCTTTGGTCACAAGTGTGGTACTATGTACAGGCCACTATGTGTAAAA
Found at i:30804 original size:21 final size:17
Alignment explanation
Indices: 30763--30797 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30753 AGTTGGTTGA
30763 ATGAGTGTGTAATGACT
1 ATGAGTGTGTAATGACT
30780 ATGAGTGTGTAATGACT
1 ATGAGTGTGTAATGACT
30797 A
1 A
30798 AGTATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (17 bp):
ATGAGTGTGTAATGACT
Found at i:38260 original size:40 final size:40
Alignment explanation
Indices: 38205--38449 Score: 356
Period size: 40 Copynumber: 6.2 Consensus size: 40
38195 CGGATGATAA
*
38205 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCC
*
38245 CGAAGGCATTTGTGCTAGTGACTA-ATCTCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATC-CGGGCTAAGTCC
*
38285 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
*
38325 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
38365 CGAAGGCATTTGTGCGAGCT-ACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCC
* * *
38405 CGAAGGCATTTGAGCGAGT-AGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTGA-CTATATCCGGGCTAAGTCC
38444 CGAAGG
1 CGAAGG
38450 TACTTGGTTT
Statistics
Matches: 196, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
39 18 0.09
40 174 0.89
41 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
Found at i:42927 original size:40 final size:40
Alignment explanation
Indices: 42890--43075 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
42880 GCTACTCGTT
* *
42890 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
42930 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
42970 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
43010 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
43051 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
43076 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:52748 original size:39 final size:40
Alignment explanation
Indices: 52705--52906 Score: 290
Period size: 39 Copynumber: 5.2 Consensus size: 40
52695 CGGATGATAA
*
52705 CGAAGGCATTTGTGCTAGTGACTAT-TCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
*
52744 CGAAGGCATTTGTGCTAGTGACTA-ATCCGGGCTAAGT-C
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
*
52782 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
52822 CGAAGGCATTTGTGCGAGCT-ACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCC
* * *
52862 CGAAGGCATTTGAGCGAGT-AGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTGA-CTATATCCGGGCTAAGTCC
52901 CGAAGG
1 CGAAGG
52907 TACTTGGTTT
Statistics
Matches: 153, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
38 23 0.15
39 65 0.42
40 64 0.42
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
Done.