Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1069
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: 21842
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Found at i:846 original size:20 final size:21
Alignment explanation
Indices: 808--850 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
798 AAAATTGTTA
808 AATTATTTTATTAAGGGGGAG
1 AATTATTTTATTAAGGGGGAG
829 AATT-TTTTGATTAAGGGGGAG
1 AATTATTTT-ATTAAGGGGGAG
850 A
1 A
851 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (21 bp):
AATTATTTTATTAAGGGGGAG
Found at i:1448 original size:21 final size:21
Alignment explanation
Indices: 1418--1471 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1408 ATCGATACAT
**
1418 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1438 TGTATGCGATACTTGAAAAGAA
1 TGTAT-CGATACATGAAAAGAA
1460 TGTATCGATACA
1 TGTATCGATACA
1472 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.18
21 16 0.57
22 7 0.25
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:2018 original size:20 final size:20
Alignment explanation
Indices: 1964--2020 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1954 AAAACCATTA
**
1964 AAAGTATCGATACACAATTC
1 AAAGTATCGATACATGATTC
*
1984 AAAGTATCGATACATGTTTC
1 AAAGTATCGATACATGATTC
*
2004 AATGTATCGATACATGA
1 AAAGTATCGATACATGA
2021 AAAAGATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACATGATTC
Found at i:2167 original size:21 final size:22
Alignment explanation
Indices: 2137--2179 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2127 CTATATTTTC
2137 AAATATGTATCGATACACTCAA
1 AAATATGTATCGATACACTCAA
*
2159 AAAT-TGTATCGATACATTCAA
1 AAATATGTATCGATACACTCAA
2180 CGGGAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (22 bp):
AAATATGTATCGATACACTCAA
Found at i:4970 original size:80 final size:79
Alignment explanation
Indices: 4832--5056 Score: 248
Period size: 80 Copynumber: 2.9 Consensus size: 79
4822 TTCTATAACC
** **
4832 GGGGATACTCCAACTTCGATTTTATTTCTAAAA-CATCAATATTT---C-ATCGGGGATACTCCA
1 GGGGATACTCCAACCACGGCTTTATTTC-AAAATCATCAAT-TTTCCACAATCGGGGATACTCCA
*
4892 ACCCCGTTATTTTCGA
64 ACCCCGTTATCTTCGA
* * *
4908 GGGGATACTCCAACCCCCGGCTTTATTTCTAAAAT-ATTAA-TTTCTCATAATCGGGGATACTCC
1 GGGGATACTCCAA-CCACGGCTTTATTTC-AAAATCATCAATTTTC-CACAATCGGGGATACTCC
4971 AACCCCGTTATCTTCGA
63 AACCCCGTTATCTTCGA
* * * *
4988 GGGGATACTCCAACCATGGTTTTATTTCCAAATCATCGATTTTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCACGGCTTTATTTCAAAATCATCAATTTTCCACAATCGGGGATACTCCAAC
5053 CCCG
66 CCCG
5057 GCTTTATTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
75 3 0.02
76 13 0.10
77 20 0.16
78 4 0.03
79 39 0.31
80 47 0.37
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCACGGCTTTATTTCAAAATCATCAATTTTCCACAATCGGGGATACTCCAAC
CCCGTTATCTTCGA
Found at i:5104 original size:52 final size:51
Alignment explanation
Indices: 4988--5157 Score: 196
Period size: 52 Copynumber: 3.3 Consensus size: 51
4978 TTATCTTCGA
** * * *
4988 GGGGATACTCCAACCATGGTTTTATTTCCAAATCATCGATTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATC
* * **
5039 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCC-ACAATC
* * * *
5091 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCACAATC
*
5143 GAGGATACTCCAACC
1 GGGGATACTCCAACC
5158 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
51 38 0.39
52 45 0.46
53 15 0.15
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:17769 original size:13 final size:13
Alignment explanation
Indices: 17751--17830 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 13
17741 ACTTTCTCTT
*
17751 AAAAAAAA-AAAG
1 AAAAAAAAGAAAA
17763 AAAAAAAAGCAAAA
1 AAAAAAAAG-AAAA
*
17777 AAAAAAAACAAAA
1 AAAAAAAAGAAAA
* *
17790 CAAAAAAACAAAA
1 AAAAAAAAGAAAA
17803 CAAAGAAAAAGAGAGAA
1 -AAA-AAAAAGA-A-AA
*
17820 AAGAAAAAGAA
1 AAAAAAAAGAA
17831 CCTGCTTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.14
13 16 0.29
14 14 0.25
15 13 0.23
16 3 0.05
17 2 0.04
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:17778 original size:18 final size:18
Alignment explanation
Indices: 17755--17826 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
17745 TCTCTTAAAA
17755 AAAAAAAGAAAAAAAAGC
1 AAAAAAAGAAAAAAAAGC
*
17773 AAAAAAA-AAAAACAAAAC
1 AAAAAAAGAAAAA-AAAGC
* *
17791 AAAAAAACAAAACAAAG-
1 AAAAAAAGAAAAAAAAGC
17808 AAAAAGAGAGAAAAGAAAA
1 AAAAA-A-AGAAAA-AAAA
17827 AGAACCTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 10 0.23
18 22 0.50
19 9 0.20
20 3 0.07
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAGC
Found at i:17827 original size:1 final size:1
Alignment explanation
Indices: 17751--17812 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
17741 ACTTTCTCTT
* ** * * * * *
17751 AAAAAAAAAAAGAAAAAAAAGCAAAAAAAAAAAACAAAACAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17813 GAGAGAAAAG
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:19134 original size:55 final size:55
Alignment explanation
Indices: 18823--19442 Score: 718
Period size: 55 Copynumber: 11.0 Consensus size: 55
18813 GATGCCTTTT
* *
18823 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACA
*
18878 CCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACG
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* * *
18937 CCTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCGGGACG
1 CC-----TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* * *
18996 CCTTTTTTTTAAAGCCCACCCAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CC----TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--C----A
* * * *
19060 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAAAGCAGGACC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* * * * *
19115 CCTTTCAAAGCGCACACAAGTTGGTGGCA-TTTTCCTGTCCACAAAGAGCATGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACA
*
19170 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACA
*
19225 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* *
19280 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACA
19335 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
* * *
19390 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
19443 TACACTTTAT
Statistics
Matches: 504, Mismatches: 36, Indels: 50
0.85 0.06 0.08
Matches are distributed among these distances:
54 10 0.02
55 280 0.56
56 13 0.03
58 52 0.10
59 72 0.14
60 53 0.11
61 19 0.04
63 4 0.01
64 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
Found at i:19185 original size:28 final size:28
Alignment explanation
Indices: 19153--19295 Score: 68
Period size: 28 Copynumber: 5.2 Consensus size: 28
19143 ATTTTCCTGT
19153 CCACAAAGAGCATGACACCTTTCAAAGC
1 CCACAAAGAGCATGACACCTTTCAAAGC
* * * * * *
19181 CCACACAAGTTG-GTGGCA-TTTTC-CAGT
1 CCACA-AAG-AGCATGACACCTTTCAAAGC
* *
19208 CCTCAAAGAGCAGGACACCTCTT-AAAGC
1 CCACAAAGAGCATGACACCT-TTCAAAGC
* * *
19236 CCACACAAGTTG-GTGGCACCTTTC--AGTC
1 CCACA-AAG-AGCATGACACCTTTCAAAG-C
*
19264 CC-CAAAGAGCAGGACACCTTTCAAAGC
1 CCACAAAGAGCATGACACCTTTCAAAGC
19291 CCACA
1 CCACA
19296 CAAGTTGGTG
Statistics
Matches: 78, Mismatches: 23, Indels: 28
0.60 0.18 0.22
Matches are distributed among these distances:
25 2 0.03
26 18 0.23
27 14 0.18
28 26 0.33
29 16 0.21
30 2 0.03
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.18
Consensus pattern (28 bp):
CCACAAAGAGCATGACACCTTTCAAAGC
Done.