Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold431
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: 33181
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:5462 original size:17 final size:18
Alignment explanation
Indices: 5440--5480 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5430 CGTTTCTTTT
5440 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
5457 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
5475 T-TTTTG
1 TCTTTTG
5481 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:5464 original size:24 final size:25
Alignment explanation
Indices: 5411--5464 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
5401 AACAAATTCT
* *
5411 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
5436 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
5459 TTTTTT
1 TTTTTT
5465 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:11774 original size:22 final size:22
Alignment explanation
Indices: 11746--11789 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11736 TTTTGAACCA
11746 TTACCATTTCATACCAAATCCC
1 TTACCATTTCATACCAAATCCC
* *
11768 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCATACCAAATCCC
11790 AAATACCAAA
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:0.27, C:0.36, G:0.02, T:0.34
Consensus pattern (22 bp):
TTACCATTTCATACCAAATCCC
Found at i:12107 original size:14 final size:12
Alignment explanation
Indices: 12087--12136 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
12077 AATAGGTACG
*
12087 TGAAAAAAAGAGT
1 TGAAAAAAA-AAT
12100 TCGAAAAAAAAAT
1 T-GAAAAAAAAAT
12113 TG-AAAAAAAAT
1 TGAAAAAAAAAT
12124 T-AAAAAAAAAT
1 TGAAAAAAAAAT
12135 TG
1 TG
12137 CATACGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 20 0.61
12 1 0.03
13 4 0.12
14 8 0.24
ACGTcount: A:0.68, C:0.02, G:0.12, T:0.18
Consensus pattern (12 bp):
TGAAAAAAAAAT
Found at i:14371 original size:16 final size:16
Alignment explanation
Indices: 14340--14391 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
14330 GAAAAGAGCG
14340 AAAATACAAAAGAAAAGA
1 AAAAT-CAAAA-AAAAGA
*
14358 AAAATGAAAAAAAAGA
1 AAAATCAAAAAAAAGA
*
14374 AAATTCAAAAAAAGAGA
1 AAAATCAAAAAAA-AGA
14391 A
1 A
14392 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 17 0.57
17 8 0.27
18 5 0.17
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.08
Consensus pattern (16 bp):
AAAATCAAAAAAAAGA
Found at i:14376 original size:15 final size:15
Alignment explanation
Indices: 14347--14397 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
14337 GCGAAAATAC
14347 AAAAGAAAAGAAAAATG
1 AAAA-AAAAG-AAAATG
*
14364 AAAAAAAAGAAAATT
1 AAAAAAAAGAAAATG
* *
14379 CAAAAAAAGAGAATG
1 AAAAAAAAGAAAATG
14394 AAAA
1 AAAA
14398 GAGAGCGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 20 0.69
16 5 0.17
17 4 0.14
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (15 bp):
AAAAAAAAGAAAATG
Found at i:14384 original size:17 final size:17
Alignment explanation
Indices: 14339--14391 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
14329 AGAAAAGAGC
* *
14339 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
14356 GAAAAAT-GAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
14372 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
14389 GAA
1 GAA
14392 TGAAAAGAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:14427 original size:15 final size:15
Alignment explanation
Indices: 14323--14432 Score: 53
Period size: 15 Copynumber: 6.9 Consensus size: 15
14313 ATCAAATGAG
14323 AGAAAAAG-AAAAGA
1 AGAAAAAGAAAAAGA
* * *
14337 GCGAAAATACAAAAGAAA
1 -AGAAAA-AGAAAA-AGA
*
14355 AGAAAAATGAAAAAAA
1 AGAAAAA-GAAAAAGA
**
14371 AGAAAATTCAAAAA-A
1 AGAAAA-AGAAAAAGA
* *
14386 AGAGAATGAAAAGAGA
1 AGAAAAAGAAAA-AGA
*
14402 GCGATAAAAGAAAAAGA
1 -AGA-AAAAGAAAAAGA
14419 AGAAAAAGAAAAAG
1 AGAAAAAGAAAAAG
14433 TGAGTGAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
14 5 0.07
15 23 0.32
16 19 0.26
17 17 0.23
18 9 0.12
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.05
Consensus pattern (15 bp):
AGAAAAAGAAAAAGA
Found at i:18302 original size:22 final size:22
Alignment explanation
Indices: 18274--18317 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18264 TTTTGAACCA
18274 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
18296 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
18318 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:20134 original size:13 final size:13
Alignment explanation
Indices: 20116--20144 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20106 AATAGTTGTG
20116 TGTTATTTAATTA
1 TGTTATTTAATTA
20129 TGTTATTTAATTA
1 TGTTATTTAATTA
20142 TGT
1 TGT
20145 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:29826 original size:47 final size:47
Alignment explanation
Indices: 29708--29876 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 47
29698 GGATGGTTGA
*
29708 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGAAT
* *
29756 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGAA-T
*
29799 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGAAT
*
29848 -C--CCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
29877 GCTTATGGCG
Statistics
Matches: 105, Mismatches: 7, Indels: 22
0.78 0.05 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 27 0.26
45 3 0.03
46 30 0.29
47 29 0.28
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGAAT
Found at i:29873 original size:44 final size:44
Alignment explanation
Indices: 29710--29884 Score: 210
Period size: 44 Copynumber: 3.9 Consensus size: 44
29700 ATGGTTGAGC
29710 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* * * *
29754 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAACTAG-GC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGA
29803 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* * *
29847 ACCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29885 CGGGTTACAT
Statistics
Matches: 111, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
43 1 0.01
44 38 0.34
45 2 0.02
46 32 0.29
47 32 0.29
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Done.