Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2175
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: 20200
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:3078 original size:20 final size:20
Alignment explanation
Indices: 3049--3123 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
3039 AAAAAGACAT
*
3049 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
3069 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
3089 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
3109 AATGTATCGATACAT
1 AATGTATCGATACAT
3124 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:3117 original size:40 final size:39
Alignment explanation
Indices: 3046--3123 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3036 GGTAAAAAGA
* *
3046 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3085 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3124 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:5977 original size:14 final size:14
Alignment explanation
Indices: 5958--5985 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5948 GGAATTTTAT
5958 GGGCCATTAGAACC
1 GGGCCATTAGAACC
5972 GGGCCATTAGAACC
1 GGGCCATTAGAACC
5986 ACTTCGCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (14 bp):
GGGCCATTAGAACC
Found at i:6769 original size:76 final size:76
Alignment explanation
Indices: 6548--6778 Score: 234
Period size: 76 Copynumber: 3.0 Consensus size: 76
6538 CAAAAGCAAG
* ** * * * * *
6548 ATGCTTTCCCAAATTCCTTAACCTTCCCAAAAGCTCAAATTGATTATCTTGCCTTCTCAAGCTTG
1 ATGCCTTCCCAAAAACCTTAACCTTCCCAAAAGTTCAAATTGATCATCTTGCATTCTTAAGCTCG
*
6613 AGAATATTGCT
66 AGAATGTTGCT
* * *
6624 ATGCCTTTCCAAAAACCTTAACCTTCCCAAATGTTCAAATTGATCATC-T-CA-CCTTTACAGGC
1 ATGCCTTCCCAAAAACCTTAACCTTCCCAAAAGTTCAAATTGATCATCTTGCATTC-TTA-A-GC
*
6686 TCAAGAATGTTGCT
63 TCGAGAATGTTGCT
** * * * *
6700 ATGCCTTCCCAAAGGCTTTAACCTTCCCAAAGGTTCAAATTGATCATCTTGTATTCTTAAACTCG
1 ATGCCTTCCCAAAAACCTTAACCTTCCCAAAAGTTCAAATTGATCATCTTGCATTCTTAAGCTCG
*
6765 AGAATGTTACT
66 AGAATGTTGCT
6776 ATG
1 ATG
6779 TCTTTCCCTA
Statistics
Matches: 126, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
73 1 0.01
74 3 0.02
75 2 0.02
76 113 0.90
77 2 0.02
78 4 0.03
79 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (76 bp):
ATGCCTTCCCAAAAACCTTAACCTTCCCAAAAGTTCAAATTGATCATCTTGCATTCTTAAGCTCG
AGAATGTTGCT
Found at i:10095 original size:17 final size:17
Alignment explanation
Indices: 10073--10106 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10063 CAGGAAACCT
10073 TAACAAAGGTCATCTGG
1 TAACAAAGGTCATCTGG
*
10090 TAACAAAGGTCTTCTGG
1 TAACAAAGGTCATCTGG
10107 ACCGATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (17 bp):
TAACAAAGGTCATCTGG
Found at i:10552 original size:3 final size:3
Alignment explanation
Indices: 10544--10571 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10534 TAAAAGTCAA
10544 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
10572 TATTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11523 original size:44 final size:41
Alignment explanation
Indices: 11460--11565 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
11450 TATAATATAC
* * *
11460 TTAATATTAATATTAATATTATTACTTATGTTATATTTATAA
1 TTAATAATAATATTTATATTATTA-TTATGTTATATTTAAAA
* *
11502 TATAATCAATAATATTTATATT-TTATTATTTTTTATTTAAAA
1 T-TAAT-AATAATATTTATATTATTATTATGTTATATTTAAAA
*
11544 TTAATAATCATATTTAT-TTATT
1 TTAATAATAATATTTATATTATT
11566 TAAATTTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
39 2 0.04
40 13 0.24
41 4 0.07
42 16 0.29
43 7 0.13
44 13 0.24
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.57
Consensus pattern (41 bp):
TTAATAATAATATTTATATTATTATTATGTTATATTTAAAA
Found at i:12339 original size:15 final size:14
Alignment explanation
Indices: 12319--12363 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
12309 TTCAAAAGCT
12319 TCACTTTTCATGTCC
1 TCACTTTT-ATGTCC
*
12334 TCACTTATTATGTCT
1 TCACTT-TTATGTCC
12349 TCACATTTTATGTCC
1 TCAC-TTTTATGTCC
12364 CCTTATAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.49
Consensus pattern (14 bp):
TCACTTTTATGTCC
Found at i:14162 original size:2 final size:2
Alignment explanation
Indices: 14155--14189 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14145 TGTCTATCTC
14155 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14190 GTAATGCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14217 original size:3 final size:3
Alignment explanation
Indices: 14204--14236 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
14194 TGCAATGTAA
*
14204 AGT AG- AGT AGT AGT AGT AAT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
14237 CCAATGGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (3 bp):
AGT
Found at i:17651 original size:2 final size:2
Alignment explanation
Indices: 17644--17678 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17634 ATGAAAAGAG
17644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17679 TTCACTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19852 original size:15 final size:18
Alignment explanation
Indices: 19822--19881 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 18
19812 ATATTATTAT
19822 TTTTTTATTTTAAATAA-
1 TTTTTTATTTTAAATAAG
19839 TTTTTTA-TTT-AATAAG
1 TTTTTTATTTTAAATAAG
19855 TTTTATCATATTTATAAATAAG
1 TTTT-T--TATTT-TAAATAAG
19877 ATTTT
1 -TTTT
19882 AATTATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.14
16 7 0.20
17 8 0.23
19 2 0.06
20 2 0.06
21 1 0.03
22 6 0.17
23 4 0.11
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTTATTTTAAATAAG
Done.