Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2692
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: 25948
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:2347 original size:12 final size:12
Alignment explanation
Indices: 2332--2364 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2322 TTAATTTAGT
*
2332 TTTTTAAAATTA
1 TTTTTAAAAATA
2344 -TTTTAAAAATA
1 TTTTTAAAAATA
2355 TTTTTAAAAA
1 TTTTTAAAAA
2365 ATACTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTTAAAAATA
Found at i:2511 original size:20 final size:19
Alignment explanation
Indices: 2463--2513 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
2453 CAAGAGAAAG
2463 TATCGATACCTTAATTAAAA
1 TATC-ATACCTTAATTAAAA
*
2483 TAT-ATACCTTAGTTAAAA
1 TATCATACCTTAATTAAAA
2501 TATCAATACCTTA
1 TATC-ATACCTTA
2514 TCCTTCAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.61
20 11 0.39
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (19 bp):
TATCATACCTTAATTAAAA
Found at i:6838 original size:155 final size:153
Alignment explanation
Indices: 6665--6960 Score: 346
Period size: 155 Copynumber: 1.9 Consensus size: 153
6655 AAAAAAGATA
* * * * *
6665 ATAAAAGGGTGAAACTATCCTAAATGCACATA-TTTGGCATGAA-GCATCCT-AGTGACTACATC
1 ATAAAAGAGTGAAACTATCCTAAAT--ACATACTCTAGCATAAACGCATCCTGA-TAACTACATC
* * * * *
6727 AAACTTGGTTTTAAAAGAAATTACTAAAATACCTTTAGGGACTACCTTCTTCTTGAAAGCATCCG
63 AAACTCGATTTTAAAA-AAATTACTAAAATACCCTTAGGGACAACCTTCATCTTG-AAGCATCCG
**
6792 GGTGACCTTAAAGGATTCGAGGATGATC
126 AATGACCTTAAAGGATTCGAGGATGATC
* * * * *
6820 ATAAAAGAGTGAACCTATCTTAAATATATACCTCTAGTATAAACGCATCCTGATAACTACATCAG
1 ATAAAAGAGTGAAACTATCCTAAATACATA-CTCTAGCATAAACGCATCCTGATAACTACATCAA
* *
6885 ACTCGATTTTAGAAAAATTACTAAAATACCCTTAGGGACAACCTTCATCTTGAAGCATCCTAATG
65 ACTCGATTTTAAAAAAATTACTAAAATACCCTTAGGGACAACCTTCATCTTGAAGCATCCGAATG
6950 ACCTTAAAGGA
130 ACCTTAAAGGA
6961 CTTGAAAATA
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
153 4 0.03
154 21 0.18
155 64 0.54
156 28 0.24
157 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (153 bp):
ATAAAAGAGTGAAACTATCCTAAATACATACTCTAGCATAAACGCATCCTGATAACTACATCAAA
CTCGATTTTAAAAAAATTACTAAAATACCCTTAGGGACAACCTTCATCTTGAAGCATCCGAATGA
CCTTAAAGGATTCGAGGATGATC
Found at i:7753 original size:21 final size:21
Alignment explanation
Indices: 7728--7770 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
7718 AAAATAATGA
*
7728 AATCACTAAT-ATTTCAACATG
1 AATCAATAATAATTT-AACATG
*
7749 AATCAATATTAATTTAACATG
1 AATCAATAATAATTTAACATG
7770 A
1 A
7771 TAATATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (21 bp):
AATCAATAATAATTTAACATG
Found at i:7777 original size:19 final size:22
Alignment explanation
Indices: 7738--7778 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
7728 AATCACTAAT
7738 ATTTCAACATGAATCAATATTA
1 ATTTCAACATGAATCAATATTA
7760 ATTT-AACATG-AT-AATATTA
1 ATTTCAACATGAATCAATATTA
7779 CAAAACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 6 0.32
22 4 0.21
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (22 bp):
ATTTCAACATGAATCAATATTA
Found at i:8200 original size:66 final size:67
Alignment explanation
Indices: 8130--8260 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 67
8120 AATCTTGGAA
*
8130 TTGCTGCACCATTACTCTGCATGACAAAACCAATGGGAATGAGAGTAGCTAAGCATAGT-CCTAG
1 TTGCTGCACCATTACTCTGCATGACAAAACCAATAGGAATGAGAGTAGCTAAGCATAGTACCTAG
8194 TG
66 TG
* * * * *
8196 TTGCTGCACTATTACTCTGCATGGCAGAACCAATAGGAATGAGAGTAGTTGAGCATAGTACCTAG
1 TTGCTGCACCATTACTCTGCATGACAAAACCAATAGGAATGAGAGTAGCTAAGCATAGTACCTAG
8261 AGCTGTCCCC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
66 53 0.91
67 5 0.09
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (67 bp):
TTGCTGCACCATTACTCTGCATGACAAAACCAATAGGAATGAGAGTAGCTAAGCATAGTACCTAG
TG
Found at i:9981 original size:17 final size:17
Alignment explanation
Indices: 9959--9992 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9949 GATAAAGTGT
9959 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
9976 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
9993 ATTTAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
TTGAAAAAAAAAAAAAA
Found at i:10022 original size:21 final size:21
Alignment explanation
Indices: 9998--10054 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
9988 AAAAAATTTA
9998 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
10019 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
10040 AATGTATCGATACAT
1 AATGTATCGATACAT
10055 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:10134 original size:19 final size:19
Alignment explanation
Indices: 10110--10177 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
10100 AATTCAACAA
10110 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
10129 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
10144 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
10161 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
10178 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:10149 original size:13 final size:13
Alignment explanation
Indices: 10131--10155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10121 ACATAAGTTT
10131 TGTATCGATACAA
1 TGTATCGATACAA
10144 TGTATCGATACA
1 TGTATCGATACA
10156 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10153 original size:32 final size:32
Alignment explanation
Indices: 10112--10174 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10102 TTCAACAATT
*
10112 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
10144 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
10175 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:10235 original size:13 final size:13
Alignment explanation
Indices: 10217--10242 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10207 CATTTTTCTG
10217 TGTATCGATACAT
1 TGTATCGATACAT
10230 TGTATCGATACAT
1 TGTATCGATACAT
10243 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:10239 original size:33 final size:33
Alignment explanation
Indices: 10197--10263 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10187 GCCAAGGAAA
***
10197 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
10230 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
10263 T
1 T
10264 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:12749 original size:27 final size:28
Alignment explanation
Indices: 12710--12785 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
12700 TTTCTTCACA
* *
12710 ATCGGGGACACTCCAACCCCGTTA-ATC
1 ATCGAGGATACTCCAACCCCGTTATATC
*
12737 ATCGAGGATACTCCAACCCCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATATC
*
12765 -TGAGAGGATACTCCAACCCCG
1 AT-CGAGGATACTCCAACCCCG
12786 ACTTTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.53
28 20 0.47
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATATC
Found at i:12780 original size:28 final size:27
Alignment explanation
Indices: 12719--12785 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
12709 AATCGGGGAC
*
12719 ACTCCAACCCCGTTAATCATCGAGGAT
1 ACTCCAACCCCGTTAATCATAGAGGAT
*
12746 ACTCCAACCCCGTTATTTC-TGAGAGGAT
1 ACTCCAACCCCGTTA-ATCAT-AGAGGAT
12774 ACTCCAACCCCG
1 ACTCCAACCCCG
12786 ACTTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.22
Consensus pattern (27 bp):
ACTCCAACCCCGTTAATCATAGAGGAT
Found at i:12832 original size:79 final size:79
Alignment explanation
Indices: 12737--12915 Score: 349
Period size: 79 Copynumber: 2.3 Consensus size: 79
12727 CCCGTTAATC
*
12737 ATCGAGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGACTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGACTTTATTTTCAAAAT
12802 ATCGATTTTTCATA
66 ATCGATTTTTCATA
12816 ATCGGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGACTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGACTTTATTTTCAAAAT
12881 ATCGATTTTTCATA
66 ATCGATTTTTCATA
12895 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
12916 ATTTTATTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 99 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGACTTTATTTTCAAAAT
ATCGATTTTTCATA
Found at i:12925 original size:51 final size:51
Alignment explanation
Indices: 12849--13017 Score: 203
Period size: 51 Copynumber: 3.3 Consensus size: 51
12839 ATTTCTGAGA
* * *
12849 GGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATCGG
1 GGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATCGG
* * * *
12900 GGATACTCCAACCCCGATTTTATTTTCACAACACCAATTTCTCCTTTAATCGG
1 GGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATCGG
** * * *
12953 GGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATCGG
13005 GGATACTCCAACC
1 GGATACTCCAACC
13018 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 35 0.36
52 18 0.19
53 33 0.34
54 11 0.11
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATCGG
Found at i:13036 original size:28 final size:28
Alignment explanation
Indices: 13000--13081 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
12990 ATTTTTCACA
*
13000 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
13028 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
13056 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
13082 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:25504 original size:14 final size:13
Alignment explanation
Indices: 25468--25512 Score: 65
Period size: 12 Copynumber: 3.4 Consensus size: 13
25458 CCTTCTCTTC
25468 AAAAAAAAAA-AA
1 AAAAAAAAAACAA
25480 AAAAAAAAAACAA
1 AAAAAAAAAACAA
25493 AAAAAACAAAACAA
1 AAAAAA-AAAACAA
25507 GAAAAA
1 -AAAAA
25513 GAGGAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.33
13 8 0.27
14 7 0.23
15 5 0.17
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:25512 original size:1 final size:1
Alignment explanation
Indices: 25468--25503 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
25458 CCTTCTCTTC
* *
25468 AAAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25504 CAAGAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.