Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1081
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: 72336
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5597 original size:23 final size:22
Alignment explanation
Indices: 5545--5597 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
5535 TCCACGTCTT
*
5545 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
5567 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
5590 TTTCTTTT
1 TTTCTTTT
5598 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:9637 original size:23 final size:22
Alignment explanation
Indices: 9585--9638 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
9575 TCCACGTCTT
*
9585 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
9607 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
9630 TTTCTTTTC
1 TTTCTTTTC
9639 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:27574 original size:20 final size:20
Alignment explanation
Indices: 27551--27597 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27541 GGGTTAAGAT
*
27551 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
27571 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
27591 TGAGCTG
1 TGAGCTG
27598 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:30407 original size:12 final size:12
Alignment explanation
Indices: 30390--30457 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 12
30380 GACTTTTCAC
30390 TTTTTTTTCTTT
1 TTTTTTTTCTTT
* **
30402 TTTTTTTGCTCAC
1 TTTTTTTTCT-TT
30415 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
30427 CTTTTTTTTGCTCT
1 -TTTTTTTT-CTTT
**
30441 TTTTTTCACTTT
1 TTTTTTTTCTTT
30453 TTTTT
1 TTTTT
30458 GAATTTTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
12 17 0.40
13 23 0.53
14 3 0.07
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:30431 original size:27 final size:25
Alignment explanation
Indices: 30386--30457 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 25
30376 GCAAGACTTT
30386 TCACTTTTTTTTCTTTTTTTTTTGC
1 TCACTTTTTTTTCTTTTTTTTTTGC
30411 TCACTTTTTTTTCTTTCTTTTTTTTGC
1 TCACTTTTTTTTC-TT-TTTTTTTTGC
*
30438 T--CTTTTTTTCACTTTTTTTT
1 TCACTTTTTTT-TCTTTTTTTT
30458 GAATTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
24 6 0.14
25 23 0.53
26 3 0.07
27 11 0.26
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (25 bp):
TCACTTTTTTTTCTTTTTTTTTTGC
Found at i:36487 original size:23 final size:22
Alignment explanation
Indices: 36435--36487 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
36425 TCCACGTCTT
*
36435 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
36457 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
36480 TTTCTTTT
1 TTTCTTTT
36488 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:50871 original size:23 final size:23
Alignment explanation
Indices: 50841--50886 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
50831 GGTTCACTTG
50841 GGTAAATTTGTAGTGGTTTATTT
1 GGTAAATTTGTAGTGGTTTATTT
50864 GGTAAATTTGTAGTGGTTTATTT
1 GGTAAATTTGTAGTGGTTTATTT
50887 TGATGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (23 bp):
GGTAAATTTGTAGTGGTTTATTT
Found at i:53337 original size:20 final size:20
Alignment explanation
Indices: 53312--53354 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53302 ATAGGTACGT
* *
53312 AAAAAAAAGAGTTCGAAAAA
1 AAAAAAAAAAATTCGAAAAA
*
53332 AAAAAAAAAAATTTGAAAAA
1 AAAAAAAAAAATTCGAAAAA
53352 AAA
1 AAA
53355 TTGAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAATTCGAAAAA
Found at i:53350 original size:12 final size:11
Alignment explanation
Indices: 53335--53365 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
53325 CGAAAAAAAA
53335 AAAAAAAATTTG
1 AAAAAAAA-TTG
53347 AAAAAAAATTG
1 AAAAAAAATTG
53358 AAAAAAAA
1 AAAAAAAA
53366 ATTGCATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:53366 original size:12 final size:12
Alignment explanation
Indices: 53334--53369 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
53324 TCGAAAAAAA
53334 AAAAAAAAATTTG
1 AAAAAAAAA-TTG
53347 -AAAAAAAATTG
1 AAAAAAAAATTG
53358 AAAAAAAAATTG
1 AAAAAAAAATTG
53370 CATACGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 19 0.86
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:55582 original size:19 final size:18
Alignment explanation
Indices: 55536--55601 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
55526 CAAATGAGAG
55536 AAAAAGAAAAGAGCGAAAATA
1 AAAAAGAAAAGA---AAAATA
*
55557 CAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAAT-A
*
55576 AAAAAGAAAAGAAAATTCA
1 AAAAAGAAAAGAAAAAT-A
55595 AAAAAGA
1 AAAAAGA
55602 GAATGAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.12
19 24 0.60
21 11 0.28
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATA
Found at i:59728 original size:21 final size:21
Alignment explanation
Indices: 59685--59747 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
59675 TTTGAACCAT
*
59685 TACCAATTT-GTACCAAATACCA
1 TACC-ATTTCGTACC-AATTCCA
59707 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
59728 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
59748 CAAATACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:61037 original size:15 final size:15
Alignment explanation
Indices: 61012--61058 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
61002 AGAAAAGAAT
61012 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
61028 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
61043 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
61058 A
1 A
61059 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:61103 original size:12 final size:12
Alignment explanation
Indices: 61086--61146 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
61076 AGTGAAAAGC
61086 AAAAAGAGATTG
1 AAAAAGAGATTG
*
61098 AAAAAGAAATTG
1 AAAAAGAGATTG
*
61110 --AAAGAG-TGG
1 AAAAAGAGATTG
*
61119 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
61131 AAAGAGAGCTTG
1 AAAAAGAGATTG
61143 AAAA
1 AAAA
61147 GAAATCGAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
9 2 0.05
10 5 0.14
11 5 0.14
12 25 0.68
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:61123 original size:21 final size:22
Alignment explanation
Indices: 61088--61137 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
61078 TGAAAAGCAA
*
61088 AAAGAGATTGAAAAAGAAATTG
1 AAAGAGATGGAAAAAGAAATTG
61110 AAAGAG-TGGAAAAAGAAATTG
1 AAAGAGATGGAAAAAGAAATTG
61131 AAAGAGA
1 AAAGAGA
61138 GCTTGAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (22 bp):
AAAGAGATGGAAAAAGAAATTG
Found at i:63039 original size:10 final size:10
Alignment explanation
Indices: 63015--63063 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
63005 AGCTCGTTTC
*
63015 CAGCTCACTT
1 CAGCTCAATT
* *
63025 GAGCTCAAGT
1 CAGCTCAATT
63035 CAGCTC-ATT
1 CAGCTCAATT
63044 CGAGCTCAATT
1 C-AGCTCAATT
63055 CAGCTCAAT
1 CAGCTCAAT
63064 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:63040 original size:20 final size:20
Alignment explanation
Indices: 63015--63061 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
63005 AGCTCGTTTC
63015 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
63035 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
63055 CAGCTCA
1 CAGCTCA
63062 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:65545 original size:11 final size:11
Alignment explanation
Indices: 65529--65561 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
65519 AGTAGTTTCT
65529 TCAAAAAAAAA
1 TCAAAAAAAAA
*
65540 TCAAAAAAAAT
1 TCAAAAAAAAA
65551 TCAAAAAAAAA
1 TCAAAAAAAAA
65562 AATTTGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:65625 original size:14 final size:15
Alignment explanation
Indices: 65603--65641 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
65593 GATATCAAGT
65603 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
65618 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
65633 TGAAAAAAA
1 TGAAAAAAA
65642 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Done.