Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold755
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: 25973
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1804 original size:32 final size:32
Alignment explanation
Indices: 1761--1822 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1751 GAGCTTTTGG
1761 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
1793 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
1823 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:13733 original size:14 final size:14
Alignment explanation
Indices: 13714--13742 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13704 ACAGATGGAT
13714 TCGTATAATTCTTA
1 TCGTATAATTCTTA
13728 TCGTATAATTCTTA
1 TCGTATAATTCTTA
13742 T
1 T
13743 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:16743 original size:15 final size:15
Alignment explanation
Indices: 16714--16775 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
16704 GTAGAAAGCC
* *
16714 TATTTTTTTTTCTAG
1 TATTTTATTTACTAG
16729 TATTTTATTTACTAG
1 TATTTTATTTACTAG
**
16744 CGTGTTTATTTACTAGCG
1 TAT-TTTATTTACTA--G
16762 TA-TTTATTTACTAG
1 TATTTTATTTACTAG
16776 CGTATTTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
14 1 0.03
15 14 0.37
16 22 0.58
18 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.58
Consensus pattern (15 bp):
TATTTTATTTACTAG
Found at i:16753 original size:16 final size:16
Alignment explanation
Indices: 16732--16782 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
16722 TTTCTAGTAT
*
16732 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
16748 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
16764 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
16780 TTT
1 TTT
16783 GCTCTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:18133 original size:13 final size:14
Alignment explanation
Indices: 18100--18133 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18090 GCCCGGAGGC
*
18100 TAAAGAAAAAGTGA
1 TAAAAAAAAAGTGA
18114 TAAAAAAAAAGTGA
1 TAAAAAAAAAGTGA
18128 TGAAAA
1 T-AAAA
18134 GTTTTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (14 bp):
TAAAAAAAAAGTGA
Found at i:19438 original size:32 final size:33
Alignment explanation
Indices: 19402--19492 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
19392 CAAAAAATAG
19402 AAATA-AATATATATATAATAATAATATATAAA
1 AAATATAATATATATATAATAATAATATATAAA
* *
19434 AAATATTAATATATAAAT-ATAAAAATATATAAA
1 AAATA-TAATATATATATAATAATAATATATAAA
* *
19467 ATATTTAGA-ATATATATAATAA-AATA
1 AAATATA-ATATATATATAATAATAATA
19493 GATATATAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 18 0.36
33 22 0.44
34 10 0.20
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (33 bp):
AAATATAATATATATATAATAATAATATATAAA
Found at i:19448 original size:30 final size:32
Alignment explanation
Indices: 19412--19492 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
19402 AAATAAATAT
*
19412 ATATATAATAATAATATATAAAAAATA-TTA-
1 ATATATAATAATAAAATATAAAAAATATTTAG
*
19442 ATATATAA-ATATAAAAATATATAAAATATTTAG
1 ATATATAATA-AT-AAAATATAAAAAATATTTAG
19475 A-ATATATATAATAAAATA
1 ATATATA-ATAATAAAATA
19493 GATATATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
29 1 0.02
30 10 0.23
31 13 0.30
32 14 0.33
33 4 0.09
34 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (32 bp):
ATATATAATAATAAAATATAAAAAATATTTAG
Found at i:19452 original size:8 final size:8
Alignment explanation
Indices: 19404--19541 Score: 77
Period size: 8 Copynumber: 16.9 Consensus size: 8
19394 AAAAATAGAA
19404 ATAAATAT
1 ATAAATAT
*
19412 ATATATA-
1 ATAAATAT
19419 ATAATAATAT
1 AT-A-AATAT
*
19429 ATAAAAAAT
1 AT-AAATAT
*
19438 ATTAATAT
1 ATAAATAT
19446 ATAAATAT
1 ATAAATAT
*
19454 AAAAATAT
1 ATAAATAT
19462 ATAAAATAT
1 AT-AAATAT
*
19471 TTAGAATAT
1 ATA-AATAT
*
19480 ATATAATAAA
1 ATA-AAT-AT
*
19490 ATAGATAT
1 ATAAATAT
*
19498 ATAGATAT
1 ATAAATAT
*
19506 ATAAATAA
1 ATAAATAT
**
19514 ATTGA-AT
1 ATAAATAT
19521 AT-AATAT
1 ATAAATAT
*
19528 -TAAATAG
1 ATAAATAT
19535 ATAAATA
1 ATAAATA
19542 AATTAAACCA
Statistics
Matches: 100, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
6 2 0.02
7 11 0.11
8 51 0.51
9 28 0.28
10 8 0.08
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (8 bp):
ATAAATAT
Found at i:19455 original size:36 final size:34
Alignment explanation
Indices: 19407--19500 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 34
19397 AATAGAAATA
19407 AATATATATATAATAATAATATATAAAAAATATT--
1 AATATATATATAA-AATAATATATAAAAAAT-TTAG
* *
19441 AATATATAAATATAAA-AATATATAAAATATTTAG
1 AATATATATATA-AAATAATATATAAAAAATTTAG
19475 AATATATATAATAAAATAGATATATA
1 AATATATAT-ATAAAATA-ATATATA
19501 GATATATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
32 2 0.04
33 13 0.25
34 24 0.47
35 5 0.10
36 7 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (34 bp):
AATATATATATAAAATAATATATAAAAAATTTAG
Found at i:19939 original size:13 final size:13
Alignment explanation
Indices: 19921--19948 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19911 GTTATTCATA
19921 ATTAATATGAATT
1 ATTAATATGAATT
19934 ATTAATATGAATT
1 ATTAATATGAATT
19947 AT
1 AT
19949 AGACTCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATTAATATGAATT
Found at i:20130 original size:19 final size:21
Alignment explanation
Indices: 20102--20151 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
20092 AAATTAAAAT
20102 TTTATATATATA-TTTAT-TA
1 TTTATATATATATTTTATATA
*
20121 TTTATCTATATATTTTATATA
1 TTTATATATATATTTTATATA
20142 TTTA-ATATAT
1 TTTATATATAT
20152 TTAATATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 10 0.37
21 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATATATATTTTATATA
Found at i:20244 original size:17 final size:17
Alignment explanation
Indices: 20222--20260 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20212 CTGACTCCAT
*
20222 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
20239 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
20256 TTTTA
1 TTTTA
20261 CATCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:20356 original size:31 final size:31
Alignment explanation
Indices: 20321--20380 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
20311 CGATCGATTT
*
20321 AATAGATTTAATATAGATTCAATTTATTTTG
1 AATAGATTTAATATAGATTAAATTTATTTTG
20352 AATAGATTTAATATAGATTAAATTTATTT
1 AATAGATTTAATATAGATTAAATTTATTT
20381 CTATTTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (31 bp):
AATAGATTTAATATAGATTAAATTTATTTTG
Found at i:20457 original size:15 final size:17
Alignment explanation
Indices: 20427--20458 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20417 GTCAAAATCT
20427 TTTTATGCAGTTATATA
1 TTTTATGCAGTTATATA
20444 TTTTATG-A-TTATATA
1 TTTTATGCAGTTATATA
20459 AATGAAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTATGCAGTTATATA
Found at i:21108 original size:18 final size:18
Alignment explanation
Indices: 21081--21123 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21071 CGCATAAAAA
* *
21081 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
21099 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
21117 GAAAGAA
1 GAAAGAA
21124 GGGGGAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:24920 original size:19 final size:19
Alignment explanation
Indices: 24875--24924 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
24865 GGGATCACTA
24875 ACTAATACTAATCTAATCT
1 ACTAATACTAATCTAATCT
24894 ACCT-ATACTAATCTAATACT
1 A-CTAATACTAATCTAAT-CT
24914 -CTAATACTAAT
1 ACTAATACTAAT
24925 AGAATAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 22 0.79
20 4 0.14
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (19 bp):
ACTAATACTAATCTAATCT
Found at i:24939 original size:14 final size:14
Alignment explanation
Indices: 24922--24949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24912 CTCTAATACT
24922 AATAGAATAGAAAA
1 AATAGAATAGAAAA
24936 AATAGAATAGAAAA
1 AATAGAATAGAAAA
24950 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Done.