Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1701
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: 37746
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:7355 original size:17 final size:17
Alignment explanation
Indices: 7333--7366 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7323 TACAATGATG
*
7333 AATGTATCGATATATTT
1 AATGTATCGATACATTT
7350 AATGTATCGATACATTT
1 AATGTATCGATACATTT
7367 CCTTGGTAGT
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:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
AATGTATCGATACATTT
Found at i:8211 original size:22 final size:24
Alignment explanation
Indices: 8158--8206 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
8148 TTAATATCGT
* *
8158 TATTATTTTCTTTCAGAATTGGTG
1 TATTTTTTTCTTTCACAATTGGTG
8182 TCAATTTTTTTCTTTCACAATTGGT
1 T--ATTTTTTTCTTTCACAATTGGT
8207 ATTTTGTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
26 20 0.95
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TATTTTTTTCTTTCACAATTGGTG
Found at i:8912 original size:22 final size:22
Alignment explanation
Indices: 8870--8912 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
8860 TTGCATGTAG
* *
8870 ATAACAATTGGTATTTATTTTA
1 ATAACAATTGGCATATATTTTA
*
8892 ATAACAATTGGCATATCTTTT
1 ATAACAATTGGCATATATTTT
8913 TAATTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
ATAACAATTGGCATATATTTTA
Found at i:14489 original size:22 final size:22
Alignment explanation
Indices: 14461--14505 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
14451 CATTTAATAG
*
14461 TGTATCGATACATCTGGGCAAA
1 TGTATCGATACATCTAGGCAAA
14483 TGTATCGATACATCTAGGCAAA
1 TGTATCGATACATCTAGGCAAA
14505 T
1 T
14506 TTGCCTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (22 bp):
TGTATCGATACATCTAGGCAAA
Found at i:14540 original size:20 final size:20
Alignment explanation
Indices: 14515--14580 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
14505 TTTGCCTGCA
14515 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
14535 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATCAG
14548 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
14568 TGTATCGATACAA
1 TGTATCGATACAA
14581 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 24 0.62
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGATCAG
Found at i:14553 original size:13 final size:13
Alignment explanation
Indices: 14535--14592 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
14525 CAAAGATCAG
14535 TGTATCGATACAA
1 TGTATCGATACAA
14548 TGTATCGATACAA
1 TGTATCGATACAA
*
14561 ---A--GAT-CAG
1 TGTATCGATACAA
14568 TGTATCGATACAA
1 TGTATCGATACAA
14581 TGTATCGATACA
1 TGTATCGATACA
14593 TTTGAGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14556 original size:33 final size:33
Alignment explanation
Indices: 14514--14592 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
14504 ATTTGCCTGC
14514 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
14547 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
14580 ATGTATCGATACA
1 ATGTATCGATACA
14593 TTTGAGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAGTGTATCGATACA
Found at i:14673 original size:13 final size:13
Alignment explanation
Indices: 14655--14679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14645 CAAAAAAATA
14655 TGTATCGATACAT
1 TGTATCGATACAT
14668 TGTATCGATACA
1 TGTATCGATACA
14680 ATACTTTATG
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:22059 original size:91 final size:91
Alignment explanation
Indices: 21953--22168 Score: 380
Period size: 91 Copynumber: 2.4 Consensus size: 91
21943 GTATTGATAC
*
21953 AATGTATCAATACAAAGCATGATGTATCGATACATCTGGACGTGTATCGATACTTTTTAGGGTTT
1 AATGTATCGATACAAAGCATGATGTATCGATACATCTGGACGTGTATCGATACTTTTTAGGGTTT
22018 TGATCATTATAGCCTAAGTCAACCTT
66 TGATCATTATAGCCTAAGTCAACCTT
*
22044 AATGTATCGATACAAAGCATGATATATCGATACATCTGGACGTGTATCGATACTTTTTAGGGTTT
1 AATGTATCGATACAAAGCATGATGTATCGATACATCTGGACGTGTATCGATACTTTTTAGGGTTT
22109 TGATCATTATAGCCTAAGTCAACCTT
66 TGATCATTATAGCCTAAGTCAACCTT
* *
22135 AATGTATCGATACAAATACCT-ATGTATCGATACA
1 AATGTATCGATACAAA-GCATGATGTATCGATACA
22169 AATACATATG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 117 0.98
92 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (91 bp):
AATGTATCGATACAAAGCATGATGTATCGATACATCTGGACGTGTATCGATACTTTTTAGGGTTT
TGATCATTATAGCCTAAGTCAACCTT
Found at i:22161 original size:20 final size:20
Alignment explanation
Indices: 22136--22187 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
22126 GTCAACCTTA
*
22136 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACAT
22156 ATGTATCGATACAAATACAT
1 ATGTATCGATACAAATACAT
22176 ATGTATCGATAC
1 ATGTATCGATAC
22188 TTTGGATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAATACAT
Found at i:24694 original size:13 final size:13
Alignment explanation
Indices: 24676--24701 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24666 TCGTAACCCT
24676 TGTATCGATACAA
1 TGTATCGATACAA
24689 TGTATCGATACAA
1 TGTATCGATACAA
24702 AGATCCTTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:24857 original size:13 final size:13
Alignment explanation
Indices: 24832--24868 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
24822 CAATCCTAAT
24832 TTAAATCATCATGA
1 TTAAAT-ATCATGA
24846 TTAAATATCATGA
1 TTAAATATCATGA
*
24859 TTAAACATCA
1 TTAAATATCA
24869 AATTCATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (13 bp):
TTAAATATCATGA
Found at i:30931 original size:13 final size:13
Alignment explanation
Indices: 30913--30938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30903 CAATTGAGTG
30913 TGTATCGATACAA
1 TGTATCGATACAA
30926 TGTATCGATACAA
1 TGTATCGATACAA
30939 AGCATAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:36242 original size:19 final size:21
Alignment explanation
Indices: 36220--36259 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
36210 AGGTGATTCG
36220 ACTC-AAAA-AAAGAAAAAAA
1 ACTCAAAAAGAAAGAAAAAAA
36239 ACTCAAAAAGAAAGAAAAAAA
1 ACTCAAAAAGAAAGAAAAAAA
36260 CCATCAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.78, C:0.10, G:0.07, T:0.05
Consensus pattern (21 bp):
ACTCAAAAAGAAAGAAAAAAA
Done.