Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3080
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: 28441
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:829 original size:17 final size:18
Alignment explanation
Indices: 790--831 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
780 AAAGAAGAAA
790 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
807 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
824 TCAAAAGA
1 ACAAAAGA
832 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:5721 original size:12 final size:12
Alignment explanation
Indices: 5690--5757 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 12
5680 TTGGAGTAAC
*
5690 AAAAAAAA-TCA
1 AAAAAAAATTCG
5701 AAAAAAAATTCG
1 AAAAAAAATTCG
*
5713 AAAAAAAATTGATTG
1 AAAAAAAA-T--TCG
5728 AAAAAAAAATTC-
1 -AAAAAAAATTCG
*
5740 AAAAAAAAGT-G
1 AAAAAAAATTCG
5751 AAAAAAA
1 AAAAAAA
5758 TCGAGCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 24 0.51
12 10 0.21
13 2 0.04
15 3 0.06
16 8 0.17
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:5743 original size:11 final size:12
Alignment explanation
Indices: 5690--5747 Score: 64
Period size: 12 Copynumber: 4.6 Consensus size: 12
5680 TTGGAGTAAC
5690 AAAAAAAA-TCA
1 AAAAAAAATTCA
5701 AAAAAAAATTCGA
1 AAAAAAAATTC-A
*
5714 AAAAAAATTGATTGA
1 AAAAAAA---ATTCA
5729 AAAAAAAATTCA
1 AAAAAAAATTCA
5741 AAAAAAA
1 AAAAAAA
5748 GTGAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 8 0.20
12 13 0.32
13 8 0.20
15 8 0.20
16 3 0.08
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:6786 original size:12 final size:12
Alignment explanation
Indices: 6769--6793 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6759 AAGAGAGAGG
6769 GTTTGAAAAAGA
1 GTTTGAAAAAGA
6781 GTTTGAAAAAGA
1 GTTTGAAAAAGA
6793 G
1 G
6794 AAGAGTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (12 bp):
GTTTGAAAAAGA
Found at i:7253 original size:22 final size:22
Alignment explanation
Indices: 7202--7267 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
7192 GGTATTTGGG
* *
7202 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
7223 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
7245 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
7268 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:11812 original size:13 final size:12
Alignment explanation
Indices: 11791--11827 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
11781 AGACCGTATG
11791 CAATTTTTTTTT
1 CAATTTTTTTTT
11803 CAATTTTTTTTT
1 CAATTTTTTTTT
11815 CAATTTTTTTTT
1 CAATTTTTTTTT
11827 C
1 C
11828 GAACTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:12194 original size:22 final size:22
Alignment explanation
Indices: 12143--12208 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
12133 GGTATTTGGG
* *
12143 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
12164 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
12186 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
12209 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:12907 original size:22 final size:22
Alignment explanation
Indices: 12879--12922 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12869 TTTTGAACCA
12879 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
12901 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
12923 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:15298 original size:11 final size:11
Alignment explanation
Indices: 15282--15315 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
15272 ATCAAATGAG
15282 AGAAAAAGAAA
1 AGAAAAAGAAA
15293 AGAAAAATGAAA
1 AGAAAAA-GAAA
15305 A-AAAAAGAAA
1 AGAAAAAGAAA
15315 A
1 A
15316 TTCAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 12 0.55
12 5 0.23
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:15310 original size:17 final size:17
Alignment explanation
Indices: 15283--15330 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
15273 TCAAATGAGA
15283 GAAAAAGAAAAGAAAAAT
1 GAAAAA-AAAAGAAAAAT
*
15301 GAAAAAAAAAGAAAATT
1 GAAAAAAAAAGAAAAAT
* *
15318 CAAAAAAAGAGAA
1 GAAAAAAAAAGAA
15331 TGAAAAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAAGAAAAAT
Found at i:18349 original size:22 final size:22
Alignment explanation
Indices: 18321--18364 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18311 TTTTGAACCA
18321 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
18343 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
18365 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:20983 original size:20 final size:20
Alignment explanation
Indices: 20958--21004 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20948 AGCTCGTTTC
20958 CAGCTCACTCAAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * * *
20978 CAGCTCATTCGAGTTCAATT
1 CAGCTCACTCAAGCTCAAGT
20998 CAGCTCA
1 CAGCTCA
21005 ATCTTAACCC
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:0.28, C:0.32, G:0.15, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27792 original size:12 final size:13
Alignment explanation
Indices: 27770--27798 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
27760 TTGTAAAGTT
27770 TTTATTTTATTTA
1 TTTATTTTATTTA
27783 TTTA-TTTATTTA
1 TTTATTTTATTTA
27795 TTTA
1 TTTA
27799 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Done.