Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2151
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: 15647
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Found at i:10326 original size:19 final size:19
Alignment explanation
Indices: 10302--10353 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
10292 CCTTCTCTTC
*
10302 AAAAAAAAAAGAGCAAAAA
1 AAAAAAAAAAGAACAAAAA
*
10321 AAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAGAACAAAAA
*
10340 AACAAAACAAAGAA
1 AA-AAAAAAAAGAA
10354 AAAGAGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.87, C:0.08, G:0.06, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAACAAAAA
Found at i:11415 original size:26 final size:26
Alignment explanation
Indices: 11385--11474 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
11375 AAGTTGGTGG
11385 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
* * * * **
11411 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCTCA-AAG-AGCAGGA
*
11440 CACTTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
11466 CACCTTTCA
1 CACCTTTCA
11475 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
25 3 0.07
26 16 0.36
27 8 0.18
28 8 0.18
29 7 0.16
30 3 0.07
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (26 bp):
CACCTTTCAGTCCTCAAAGAGCAGGA
Found at i:12131 original size:56 final size:56
Alignment explanation
Indices: 11338--12201 Score: 818
Period size: 55 Copynumber: 15.3 Consensus size: 56
11328 TCCGCTTTTT
11338 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
11393 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
11448 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACC-TTC
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
11502 AGTCCGCAAAGAGCAGGACCCCTCTTAAAAGCCCACACAAGTTTGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
11558 AGTCCTCAAAGAGCAGACACACCGT-TTCAAA-CACCACCCAAGTTTTTTTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAG-GACACC-TCTTCAAAGC-CCACACAAG------TTGGTGGCACCTTT-
11620 C
56 C
*
11621 AAGTCCTCAAAGAGCAGG-CACCTCTT-AAAGCCCACAC-AG-TGGTGGGACAGCCTTCC
1 -AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGT-GG-CA-CCTTTC
* * *
11677 AATCC-CAAAG-GCAGGACAAACCTC-TC-AAGCCCACACGAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGAC--ACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
11731 AAGTCCTCAAAAGAGCAAGGACACCCTCTTAAAAAGCCCACACAAGTT-GTGGCACCTTTCC
1 -AGTCCTC-AAAGAGC-AGGACA-CCTCTT-CAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
11792 AGTCCTTCAAAGA-CAGGACACCTCTT--AAGCCCACACAAGTTTGGTGGCGCCTTCC
1 AGTCC-TCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAG-TTGGTGGCACCTTTC
* *
11847 TAGTCCAGC-AAGAGCAGGACAACCTC-TCAAAG-CCACACAA-ATGGTGGCACC-TTC
1 -AGTCC-TCAAAGAGCAGGAC-ACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
11901 AGTCCCCGAAGGAGCAGAAACACCT-TTCAAAGCCCCCACAAGTTGG-GTGCA-TTTTCC
1 AGTCCTC-AAAGAGCAG-GACACCTCTTCAAAGCCCACACAAGTTGGTG-GCACCTTT-C
* * * **
11958 A-TCCTCAAAGAGCA-GACACCTTTTAAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*** * *
12012 AGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
12073 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACTAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACAC-AAGTTGGTGGCACCTTTC
* * * *
12129 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
12184 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
12202 TACACTTTAT
Statistics
Matches: 681, Mismatches: 63, Indels: 130
0.78 0.07 0.15
Matches are distributed among these distances:
52 1 0.00
53 20 0.03
54 95 0.14
55 243 0.36
56 119 0.17
57 49 0.07
58 17 0.02
59 8 0.01
60 22 0.03
61 72 0.11
62 10 0.01
63 9 0.01
64 16 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (56 bp):
AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:12885 original size:21 final size:21
Alignment explanation
Indices: 12819--12896 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
12809 AAAAAAATTC
*
12819 CAAATGTATCGATACATT-TGT
1 CAAATGTATCGATACATTCT-A
**
12840 TGAATGTATCGATACATTC-A
1 CAAATGTATCGATACATTCTA
12860 CAAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCTA
12881 CAAATGTATCGATACA
1 CAAATGTATCGATACA
12897 GGGTCCACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 17 0.34
21 33 0.66
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:12887 original size:41 final size:40
Alignment explanation
Indices: 12815--12896 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
12805 AAAAAAAAAA
***
12815 ATTCCAAATGTATCGATACATTTGTTGAATGTATCGATAC
1 ATTCCAAATGTATCGATACATTTGACAAATGTATCGATAC
12855 ATTCACAAATGTATCGATACATTCT-ACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATT-TGACAAATGTATCGATAC
12896 A
1 A
12897 GGGTCCACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 4 0.11
41 32 0.86
42 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTTGACAAATGTATCGATAC
Found at i:12955 original size:19 final size:19
Alignment explanation
Indices: 12931--12999 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
12921 AATTCAACGA
12931 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
12950 TTTGTATCGATACA-CA--
1 TTTGTATCGATACATAAGT
*
12966 --TGTAGCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
12983 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
13000 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 11 0.27
15 1 0.02
18 1 0.02
19 28 0.68
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:12975 original size:33 final size:33
Alignment explanation
Indices: 12933--12996 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
12923 TTCAACGATT
* *
12933 TGTATCGATACATAAGTTTTGTATCGATACACA
1 TGTAGCGATACATAAGTATTGTATCGATACACA
12966 TGTAGCGATACATAAGTATTGTATCGATACA
1 TGTAGCGATACATAAGTATTGTATCGATACA
12997 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTAGCGATACATAAGTATTGTATCGATACACA
Found at i:13057 original size:13 final size:13
Alignment explanation
Indices: 13039--13064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13029 CATTTTTCTG
13039 TGTATCGATACAT
1 TGTATCGATACAT
13052 TGTATCGATACAT
1 TGTATCGATACAT
13065 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13061 original size:33 final size:33
Alignment explanation
Indices: 13019--13085 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
13009 GCCAAGGAAA
***
13019 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
13052 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
13085 T
1 T
13086 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:15603 original size:28 final size:27
Alignment explanation
Indices: 15536--15608 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
15526 CTTCACAATC
* *
15536 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
15563 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
15591 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
15609 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Done.