Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1198
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: 31995
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Found at i:958 original size:22 final size:22
Alignment explanation
Indices: 930--973 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
920 CAAAGCTCAT
*
930 GATATAATTTACTTTTTAATAA
1 GATATAAATTACTTTTTAATAA
*
952 GATATAAATTACTTTTTGATAA
1 GATATAAATTACTTTTTAATAA
974 ATTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
GATATAAATTACTTTTTAATAA
Found at i:2085 original size:14 final size:14
Alignment explanation
Indices: 2066--2092 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2056 GCTCTACACC
2066 ACAAACAAACAAAT
1 ACAAACAAACAAAT
2080 ACAAACAAACAAA
1 ACAAACAAACAAA
2093 AAATGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.22, G:0.00, T:0.04
Consensus pattern (14 bp):
ACAAACAAACAAAT
Found at i:2656 original size:51 final size:52
Alignment explanation
Indices: 2597--2731 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 52
2587 GAAAGAAAGC
*
2597 GTATCGATATATT-TTTATTTGTATCGATACATTCTTGG-TTTTGACCCAAAA
1 GTATCGATATATTCTTTA-TTGTATCGATACATTCTAGGTTTTTGACCCAAAA
* *
2648 GTATCGATATATTCATTATTGTATCGATACATTCTAGGTTTTTGACCCAAAT
1 GTATCGATATATTCTTTATTGTATCGATACATTCTAGGTTTTTGACCCAAAA
* * * *
2700 GTATTGATACATTCTTCAATGTATCGATACAT
1 GTATCGATATATTCTTTATTGTATCGATACAT
2732 CCACTTAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 32 0.43
52 42 0.57
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (52 bp):
GTATCGATATATTCTTTATTGTATCGATACATTCTAGGTTTTTGACCCAAAA
Found at i:6910 original size:79 final size:79
Alignment explanation
Indices: 6426--6918 Score: 301
Period size: 79 Copynumber: 6.2 Consensus size: 79
6416 GTGAAAATTA
* ** * * * *
6426 GGGTTGGAGTATCCCCTCGGAGATGGT-GAGATTGGAGTATCCC-C-ATGATGAAAATTTTAATA
1 GGGTTGAAGTATCCCCTCAAAAATGATGGAG-TTGGAGTA-CCCTCGATGGTGAAAA-TTTGATA
6488 TTTTGAAAGTAAAAACG
63 TTTTGAAAGTAAAAACG
* * * * * * *
6505 AGGTTGAAGTATCCTCTCAGAAATGATAGGA-TTAGTGTATCCTCGATGGTGAAAAATTTAATAT
1 GGGTTGAAGTATCCCCTCAAAAATGAT-GGAGTTGGAGTACCCTCGATGGTG-AAAATTTGATAT
*
6569 TTTGGAAGTAAAAACG
64 TTTGAAAGTAAAAACG
* * * * ** *
6585 AGGTCAGGTCAGAGTAT-CCCTTAAAAATGATGGGGTT-GAGTATACTCGATGGTGAAAATTCGA
1 -GG---GTTGA-AGTATCCCCTCAAAAATGATGGAGTTGGAGTACCCTCGATGGTGAAAATTTGA
* *
6648 TATTTTAAAAATAAAAACTG
61 TATTTTGAAAGTAAAAAC-G
* * ** * * *
6668 GGTTTG-AGTATCCACTGGAAAATGAT-GAGGTTGGAGTATTCC-CAATGATGAAAATTTGATAT
1 GGGTTGAAGTATCCCCTCAAAAATGATGGA-GTTGGAGTA-CCCTCGATGGTGAAAATTTGATAT
* * *
6730 TTTGGAGGTAAAAACA
64 TTTGAAAGTAAAAACG
* * * * * *
6746 GGG-TCAGAGTAT-CCCTGCAAAAATAATGGGGTTGGAGTATCCCT-AATAGTAAAAAATTTGAT
1 GGGTTGA-AGTATCCCCT-CAAAAATGATGGAGTTGGAGTA-CCCTCGATGGT-GAAAATTTGAT
* **
6808 ATTTTGGAAGTAAAAATA
62 ATTTTGAAAGTAAAAACG
* * *
6826 TGGTTGAAGTATCCCCT-AAAAATGATGGAGTTGTAGTACCCTTGATGGTGAAAATTTTGATATT
1 GGGTTGAAGTATCCCCTCAAAAATGATGGAGTTGGAGTACCCTCGATGGTGAAAA-TTTGATATT
*
6890 TTGAAAGTAAAAATG
65 TTGAAAGTAAAAACG
*
6905 GGGTTGGAGTATCC
1 GGGTTGAAGTATCC
6919 TGATAGGTTA
Statistics
Matches: 322, Mismatches: 66, Indels: 52
0.73 0.15 0.12
Matches are distributed among these distances:
77 7 0.02
78 29 0.09
79 146 0.45
80 64 0.20
81 13 0.04
82 24 0.07
83 18 0.06
84 16 0.05
85 5 0.02
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (79 bp):
GGGTTGAAGTATCCCCTCAAAAATGATGGAGTTGGAGTACCCTCGATGGTGAAAATTTGATATTT
TGAAAGTAAAAACG
Found at i:19588 original size:1 final size:1
Alignment explanation
Indices: 19578--19730 Score: 135
Period size: 1 Copynumber: 153.0 Consensus size: 1
19568 TGGCAATTGG
* * * ** * * *
19578 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAACAAAAAAAAAAACAAAACAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * ** * * * * *
19643 AAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
19708 AAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
19731 GTGAAGATTT
Statistics
Matches: 118, Mismatches: 34, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 118 1.00
ACGTcount: A:0.88, C:0.07, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:19608 original size:29 final size:29
Alignment explanation
Indices: 19576--19728 Score: 173
Period size: 29 Copynumber: 5.0 Consensus size: 29
19566 CATGGCAATT
19576 GGAAAAAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAA
*
19605 GGAAAAACAAAAAAAAAAACAAAACAAAAAAAA
1 GG---AA-AAAGAAAAAAACAAAACAAAAAAAA
**
19638 AAAAAAAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAA
19667 GGAAAAAGAAAGAAAAAAAACAAAACAAAAAAAA
1 GG---AA-AAAG-AAAAAAACAAAACAAAAAAAA
* *
19701 -GAAAAAAAAAAAAAAAAAACAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAA
19729 AAGTGAAGAT
Statistics
Matches: 107, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
28 20 0.19
29 29 0.27
30 4 0.04
32 4 0.04
33 29 0.27
34 21 0.20
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (29 bp):
GGAAAAAGAAAAAAACAAAACAAAAAAAA
Found at i:19626 original size:33 final size:32
Alignment explanation
Indices: 19578--19730 Score: 215
Period size: 33 Copynumber: 4.8 Consensus size: 32
19568 TGGCAATTGG
*
19578 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAA
1 AAAAAAAAAAAAACAAAACAAAAAAAAGGAAA
19610 AACAAAAAAAAAAACAAAAC-AAAAAAA--AAA
1 AA-AAAAAAAAAAACAAAACAAAAAAAAGGAAA
*
19640 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAA
1 AAAAAAAAAAAAACAAAACAAAAAAAAGGAAA
*
19672 AAGAAAGAAAAAAAACAAAACAAAAAAAAGAAAAA
1 AA-AAA-AAAAAAAACAAAACAAAAAAAAG-GAAA
19707 AAAAAAAAAAAAACAAAA-AAAAAA
1 AAAAAAAAAAAAACAAAACAAAAAA
19731 GTGAAGATTT
Statistics
Matches: 110, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.15
30 12 0.11
32 20 0.18
33 32 0.29
34 25 0.23
35 5 0.05
ACGTcount: A:0.88, C:0.07, G:0.06, T:0.00
Consensus pattern (32 bp):
AAAAAAAAAAAAACAAAACAAAAAAAAGGAAA
Found at i:19648 original size:62 final size:64
Alignment explanation
Indices: 19578--19728 Score: 265
Period size: 62 Copynumber: 2.4 Consensus size: 64
19568 TGGCAATTGG
19578 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAACAAA-AAAAAAAACAAAACAAAAAAAA-AA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAACAAAGAAAAAAAACAAAACAAAAAAAAGAA
*
19640 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAAAGAA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAACAAAGAAAAAAAACAAAACAAAAAAAAGAA
19704 AAAAA-AAAAAAA-AAAACAAAAAAAA
1 AAAAAGAAAAAAACAAAACAAAAAAAA
19729 AAGTGAAGAT
Statistics
Matches: 86, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
62 50 0.58
63 29 0.34
64 7 0.08
ACGTcount: A:0.87, C:0.07, G:0.06, T:0.00
Consensus pattern (64 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAACAAAGAAAAAAAACAAAACAAAAAAAAGAA
Found at i:25083 original size:1 final size:1
Alignment explanation
Indices: 25077--25127 Score: 66
Period size: 1 Copynumber: 51.0 Consensus size: 1
25067 TGGCAATTGG
* * * *
25077 AAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25128 GTGAAGATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.92, C:0.02, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:25092 original size:11 final size:11
Alignment explanation
Indices: 25076--25127 Score: 81
Period size: 11 Copynumber: 4.8 Consensus size: 11
25066 ATGGCAATTG
25076 GAAAAAAAAAA
1 GAAAAAAAAAA
25087 GAAAAAAAAAA
1 GAAAAAAAAAA
25098 G-AAAAAAAAA
1 GAAAAAAAAAA
25108 GAAAAAAAAACA
1 GAAAAAAAAA-A
25120 -AAAAAAAA
1 GAAAAAAAA
25128 GTGAAGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.26
11 28 0.72
12 1 0.03
ACGTcount: A:0.90, C:0.02, G:0.08, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:25093 original size:10 final size:10
Alignment explanation
Indices: 25078--25128 Score: 84
Period size: 10 Copynumber: 5.0 Consensus size: 10
25068 GGCAATTGGA
25078 AAAAAAAAAG
1 AAAAAAAAAG
25088 AAAAAAAAAAG
1 -AAAAAAAAAG
25099 AAAAAAAAAG
1 AAAAAAAAAG
*
25109 AAAAAAAAAC
1 AAAAAAAAAG
25119 AAAAAAAAAG
1 AAAAAAAAAG
25129 TGAAGATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
10 28 0.74
11 10 0.26
ACGTcount: A:0.90, C:0.02, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:27082 original size:24 final size:24
Alignment explanation
Indices: 27046--27105 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
27036 TTTGGTAAGA
* *
27046 TTGATTTTCATTTA-ACTTGATAAT
1 TTGATTTTTATTTATA-TTAATAAT
27070 TTGATTTTTATTTATATTAATAAT
1 TTGATTTTTATTTATATTAATAAT
* *
27094 TTTACTTTTATT
1 TTGATTTTTATT
27106 AATCGCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (24 bp):
TTGATTTTTATTTATATTAATAAT
Found at i:30682 original size:16 final size:17
Alignment explanation
Indices: 30661--30702 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
30651 CTTTTCATAA
30661 AATATAAAAATA-AAAT
1 AATATAAAAATATAAAT
* *
30677 AATATAATAATATAATT
1 AATATAAAAATATAAAT
30694 AAT-TAAAAA
1 AATATAAAAA
30703 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAAAAATATAAAT
Done.