Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2087
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: 27696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2863 original size:21 final size:21
Alignment explanation
Indices: 2839--2885 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2829 TTTAATGCTG
2839 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
2859 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
2880 ATTTTG
1 ATTTTG
2886 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:3024 original size:13 final size:13
Alignment explanation
Indices: 3006--3044 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2996 ATAATCACCC
*
3006 TGTATCGATACAG
1 TGTATCGATACAA
3019 TGTATCGATACAA
1 TGTATCGATACAA
3032 TGTATCGATACAA
1 TGTATCGATACAA
3045 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3055 original size:20 final size:20
Alignment explanation
Indices: 3030--3108 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
3020 GTATCGATAC
3030 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3050 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
3075 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
3095 CATGTATCGATACA
1 AATGTATCGATACA
3109 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:5143 original size:15 final size:15
Alignment explanation
Indices: 5123--5153 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5113 ATTTCGTTTG
*
5123 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5138 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5153 G
1 G
5154 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:6985 original size:21 final size:21
Alignment explanation
Indices: 6956--7000 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6946 AAGTTTTCAT
*
6956 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
6976 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
6998 TTT
1 TTT
7001 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:9238 original size:13 final size:13
Alignment explanation
Indices: 9220--9245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9210 CAATTTTTTG
9220 TGTATCGATACAT
1 TGTATCGATACAT
9233 TGTATCGATACAT
1 TGTATCGATACAT
9246 ACTTGCTGTA
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:9697 original size:13 final size:13
Alignment explanation
Indices: 9681--9705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9671 CAATTAATCA
9681 TGTATCGATACAT
1 TGTATCGATACAT
9694 TGTATCGATACA
1 TGTATCGATACA
9706 ATGGACCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9698 original size:33 final size:33
Alignment explanation
Indices: 9661--9725 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
9651 TTTGAAGCAA
* *
9661 TGTATCAATACAATTAATCATGTATCGATACAT
1 TGTATCAATACAATGAACCATGTATCGATACAT
* *
9694 TGTATCGATACAATGGACCATGTATCGATACA
1 TGTATCAATACAATGAACCATGTATCGATACA
9726 AATAGTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCAATACAATGAACCATGTATCGATACAT
Found at i:14229 original size:20 final size:20
Alignment explanation
Indices: 14204--14254 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
14194 GAAGGAAATA
* * *
14204 TATCGATACATTTTTCATTT
1 TATCGATACATTCTTCAATG
*
14224 TATCGAGACATTCTTCAATG
1 TATCGATACATTCTTCAATG
*
14244 TATCAATACAT
1 TATCGATACAT
14255 ACAACCAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:16594 original size:20 final size:19
Alignment explanation
Indices: 16569--16702 Score: 157
Period size: 20 Copynumber: 6.7 Consensus size: 19
16559 GTTAGAAGCA
*
16569 ATGTATCGATACGATTCCTT
1 ATGTATCGATACAATTCC-T
16589 ATGTATCGATACAATGTACC-
1 ATGTATCGATACAAT-T-CCT
16609 ATGTATCGATACAATTCCTT
1 ATGTATCGATACAATTCC-T
16629 ATGTATCGATACAATGTACC-
1 ATGTATCGATACAAT-T-CCT
16649 ATGTATCGATACAATTCCAT
1 ATGTATCGATACAATTCC-T
16669 ATGTATCGATACAATGTACC-
1 ATGTATCGATACAAT-T-CCT
16689 ATGTATCGATACAA
1 ATGTATCGATACAA
16703 ACAATGGTAG
Statistics
Matches: 103, Mismatches: 1, Indels: 20
0.83 0.01 0.16
Matches are distributed among these distances:
18 4 0.04
19 2 0.02
20 88 0.85
21 3 0.03
22 6 0.06
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACAATTCCT
Found at i:16626 original size:40 final size:40
Alignment explanation
Indices: 16569--16702 Score: 250
Period size: 40 Copynumber: 3.4 Consensus size: 40
16559 GTTAGAAGCA
*
16569 ATGTATCGATACGATTCCTTATGTATCGATACAATGTACC
1 ATGTATCGATACAATTCCTTATGTATCGATACAATGTACC
16609 ATGTATCGATACAATTCCTTATGTATCGATACAATGTACC
1 ATGTATCGATACAATTCCTTATGTATCGATACAATGTACC
*
16649 ATGTATCGATACAATTCCATATGTATCGATACAATGTACC
1 ATGTATCGATACAATTCCTTATGTATCGATACAATGTACC
16689 ATGTATCGATACAA
1 ATGTATCGATACAA
16703 ACAATGGTAG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 92 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (40 bp):
ATGTATCGATACAATTCCTTATGTATCGATACAATGTACC
Found at i:16775 original size:19 final size:19
Alignment explanation
Indices: 16731--16803 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
16721 CTGCCAGTTT
**
16731 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
16751 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
16770 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
16791 -ATGTATCGATACA
1 CATGTATCGATACA
16804 TCTCAGTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:19315 original size:13 final size:13
Alignment explanation
Indices: 19297--19323 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19287 ATAGTAACCC
19297 ATGTATCGATACA
1 ATGTATCGATACA
19310 ATGTATCGATACA
1 ATGTATCGATACA
19323 A
1 A
19324 GGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21438 original size:21 final size:20
Alignment explanation
Indices: 21388--21444 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
21378 GGCAGTAGCC
21388 AAAATTGTATCGATACACAA
1 AAAATTGTATCGATACACAA
**
21408 AGTA-TGTATCGATACACAAA
1 AAAATTGTATCGATACAC-AA
21428 AAAATTGTATCGATACA
1 AAAATTGTATCGATACA
21445 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 13 0.42
20 6 0.19
21 12 0.39
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (20 bp):
AAAATTGTATCGATACACAA
Found at i:27625 original size:13 final size:13
Alignment explanation
Indices: 27607--27645 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
27597 ACATTTTTCT
27607 TTGTATCGATACA
1 TTGTATCGATACA
27620 TTGTATCGATACA
1 TTGTATCGATACA
* *
27633 CTGTATCAATACA
1 TTGTATCGATACA
27646 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Done.