Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1878
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: 29593
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:2470 original size:10 final size:10
Alignment explanation
Indices: 2448--2504 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
2438 CTTCCAATTT
*
2448 AGCTC-AATG
1 AGCTCAAATC
2457 AGCTCAAATC
1 AGCTCAAATC
* *
2467 AGCTCAATTT
1 AGCTCAAATC
2477 AGCTCAAATC
1 AGCTCAAATC
* *
2487 AGCTCAATTT
1 AGCTCAAATC
2497 AGCTCAAA
1 AGCTCAAA
2505 ACTTGCAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
9 5 0.13
10 34 0.87
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:2482 original size:20 final size:20
Alignment explanation
Indices: 2448--2504 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2438 CTTCCAATTT
*
2448 AGCTCAA-TGAGCTCAAATC
1 AGCTCAATTTAGCTCAAATC
2467 AGCTCAATTTAGCTCAAATC
1 AGCTCAATTTAGCTCAAATC
2487 AGCTCAATTTAGCTCAAA
1 AGCTCAATTTAGCTCAAA
2505 ACTTGCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 7 0.19
20 29 0.81
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (20 bp):
AGCTCAATTTAGCTCAAATC
Found at i:2493 original size:30 final size:29
Alignment explanation
Indices: 2442--2503 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
2432 AATTAACTTC
*
2442 CAATTTAGCTCAATGAGCTCAAATCAGCT
1 CAATTTAGCTCAATCAGCTCAAATCAGCT
* *
2471 CAATTTAGCTCAAATCAGCTCAATTTAGCT
1 CAATTTAGCTC-AATCAGCTCAAATCAGCT
2501 CAA
1 CAA
2504 AACTTGCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (29 bp):
CAATTTAGCTCAATCAGCTCAAATCAGCT
Found at i:3595 original size:10 final size:10
Alignment explanation
Indices: 3580--3641 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
3570 TTTGAACCAT
*
3580 TACCAATTCG
1 TACCAATTCA
*
3590 TACCAAATACCA
1 TACC-AAT-TCA
*
3602 TACCATTTCA
1 TACCAATTCA
3612 TACCAATTCCA
1 TACCAATT-CA
* *
3623 TACCATTTCG
1 TACCAATTCA
3633 TACCAATTC
1 TACCAATTC
3642 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:3625 original size:21 final size:21
Alignment explanation
Indices: 3580--3642 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
3570 TTTGAACCAT
* *
3580 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
3602 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
3623 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
3643 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:3959 original size:14 final size:15
Alignment explanation
Indices: 3940--3975 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
3930 ATAGGTACGT
*
3940 AAAAAAATTGAAAA-
1 AAAAAAATTCAAAAG
3954 AAAAAAATTCAAAAG
1 AAAAAAATTCAAAAG
3969 AAAAAAA
1 AAAAAAA
3976 AAATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAAAATTCAAAAG
Found at i:3974 original size:18 final size:18
Alignment explanation
Indices: 3951--3993 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3941 AAAAAATTGA
3951 AAAAAAAAAATTCAAAAG
1 AAAAAAAAAATTCAAAAG
**
3969 AAAAAAAAAATTTGAAAG
1 AAAAAAAAAATTCAAAAG
3987 AAAAAAA
1 AAAAAAA
3994 TTGTATACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAAAAAATTCAAAAG
Found at i:3985 original size:14 final size:15
Alignment explanation
Indices: 3940--3995 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
3930 ATAGGTACGT
*
3940 AAAAAAA-TTGAAAA
1 AAAAAAATTTGAAAG
**
3954 AAAAAAATTCAAAAG
1 AAAAAAATTTGAAAG
3969 AAAAAAAAAATTTGAAAG
1 ---AAAAAAATTTGAAAG
3987 AAAAAAATT
1 AAAAAAATT
3996 GTATACGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
18 13 0.39
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (15 bp):
AAAAAAATTTGAAAG
Found at i:6200 original size:19 final size:19
Alignment explanation
Indices: 6172--6223 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
6162 GAGAAAATAC
*
6172 AAAAGAAAAGAAAAATGAAA
1 AAAAG-AAAGAAAAATCAAA
*
6192 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAAATCAAA
* *
6211 AAGAGAATGAAAA
1 AAAAGAAAGAAAA
6224 GAGAGCGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAGAAAGAAAAATCAAA
Found at i:6262 original size:14 final size:15
Alignment explanation
Indices: 6233--6262 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6223 AGAGAGCGAG
6233 AAAAGAAAAAGATGA
1 AAAAGAAAAAGATGA
6248 AAAAGAAAAAG-TGA
1 AAAAGAAAAAGATGA
6262 A
1 A
6263 TGAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGATGA
Found at i:10330 original size:10 final size:10
Alignment explanation
Indices: 10315--10376 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
10305 TTTGAACCAT
*
10315 TACCAATTCG
1 TACCAATTCA
*
10325 TACCAAATACCA
1 TACC-AAT-TCA
*
10337 TACCATTTCA
1 TACCAATTCA
10347 TACCAATTCCA
1 TACCAATT-CA
* *
10358 TACCATTTCG
1 TACCAATTCA
10368 TACCAATTC
1 TACCAATTC
10377 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:10360 original size:21 final size:21
Alignment explanation
Indices: 10315--10377 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
10305 TTTGAACCAT
* *
10315 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
10337 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
10358 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
10378 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:12714 original size:23 final size:22
Alignment explanation
Indices: 12662--12714 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
12652 TCCACGTCTT
*
12662 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
12684 -TTCATTTTCTCTTCTTTTT-TCAA
1 TTTC-TTTTCT-TTCTTTTTCT-AA
12707 TTTCTTTT
1 TTTCTTTT
12715 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 6 0.23
23 14 0.54
24 3 0.12
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:22224 original size:14 final size:14
Alignment explanation
Indices: 22200--22252 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
22190 GGATATCAAG
22200 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
22213 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
22226 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
22240 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
22253 GAGAGCTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
12 2 0.05
13 12 0.32
14 24 0.63
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:22229 original size:26 final size:28
Alignment explanation
Indices: 22200--22252 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
22190 GGATATCAAG
22200 TTGTG-AAAAAAAATT-TGAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAA
22226 TTGTGAAAAAAAAATTGTGAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAA
22253 GAGAGCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 5 0.20
27 10 0.40
28 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (28 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAAA
Done.