Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 12 of 12
Found at i:1680385 original size:22 final size:23
Alignment explanation
Indices: 1680358--1680414 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
1680348 GCCATGGATG
* *
1680358 AAAAATAAATGTCT-TTTTTTAA
1 AAAAATAAATGTATATGTTTTAA
*
1680380 AAAAATTAATGTATGATGTTTTAA
1 AAAAATAAATGTAT-ATGTTTTAA
1680404 AAAAATTAAAT
1 AAAAA-TAAAT
1680415 TAAAGTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 12 0.43
24 12 0.43
25 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (23 bp):
AAAAATAAATGTATATGTTTTAA
Found at i:1680829 original size:18 final size:18
Alignment explanation
Indices: 1680772--1680832 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 18
1680762 ATAAATTATG
*
1680772 TAAAATAT-AAAATTAAT
1 TAAAATATAAAAAATAAT
* *
1680789 TAAGATATAAAACA-AA-
1 TAAAATATAAAAAATAAT
* *
1680805 CATAATATAAAAAATAAT
1 TAAAATATAAAAAATAAT
1680823 TAAAATATAA
1 TAAAATATAA
1680833 TATAAAAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
16 10 0.31
17 11 0.34
18 11 0.34
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAATATAAAAAATAAT
Found at i:1680831 original size:34 final size:34
Alignment explanation
Indices: 1680775--1680848 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
1680765 AATTATGTAA
* * *
1680775 AATAT-AAAATTAATTAAGATATAAAACAAACAT
1 AATATAAAAAATAATTAAAATATAAAACAAAAAT
* *
1680808 AATATAAAAAATAATTAAAATATAATATAAAAAT
1 AATATAAAAAATAATTAAAATATAAAACAAAAAT
1680842 AATATAA
1 AATATAA
1680849 TTATAATACA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 5 0.14
34 30 0.86
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (34 bp):
AATATAAAAAATAATTAAAATATAAAACAAAAAT
Found at i:1680845 original size:11 final size:11
Alignment explanation
Indices: 1680775--1680848 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
1680765 AATTATGTAA
*
1680775 AATATAAAATT
1 AATATAAAAAT
*
1680786 AAT-TAAGATAT
1 AATATAA-AAAT
* * *
1680797 AAAACAAACAT
1 AATATAAAAAT
1680808 AATATAAAAAAT
1 AATAT-AAAAAT
1680820 AAT-TAAAATAT
1 AATATAAAA-AT
1680831 AATATAAAAAT
1 AATATAAAAAT
1680842 AATATAA
1 AATATAA
1680849 TTATAATACA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
10 7 0.14
11 28 0.56
12 15 0.30
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1682801 original size:2 final size:2
Alignment explanation
Indices: 1682788--1682832 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1682778 TATGATTAAA
* * * *
1682788 AT AT AT AA AT AT AT AT AC AA AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1682830 AT A
1 AT A
1682833 GATTACAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1682802 original size:10 final size:10
Alignment explanation
Indices: 1682727--1682832 Score: 59
Period size: 10 Copynumber: 11.3 Consensus size: 10
1682717 CATGATCAGA
*
1682727 ATATAAATAC
1 ATATAAATAT
* *
1682737 ATAGACATAT
1 ATATAAATAT
*
1682747 -TA-AAATTT
1 ATATAAATAT
1682755 ATAT-AAT-T
1 ATATAAATAT
1682763 ATAT-AATAT
1 ATATAAATAT
*
1682772 -TTTAAATAT
1 ATATAAATAT
1682781 GAT-TAAA-AT
1 -ATATAAATAT
1682790 ATATAAATAT
1 ATATAAATAT
1682800 ATATACAA-AT
1 ATATA-AATAT
**
1682810 ATATATTTAT
1 ATATAAATAT
*
1682820 ATATATATAT
1 ATATAAATAT
1682830 ATA
1 ATA
1682833 GATTACAAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
8 16 0.21
9 19 0.25
10 39 0.51
11 3 0.04
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (10 bp):
ATATAAATAT
Found at i:1682809 original size:20 final size:19
Alignment explanation
Indices: 1682743--1682824 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
1682733 ATACATAGAC
*
1682743 ATAT-TAAAATTTATATAAT
1 ATATATAAAATATATA-AAT
* *
1682762 -TATATAATAT-TTTAAAT
1 ATATATAAAATATATAAAT
1682779 ATGAT-TAAAATATATAAAT
1 AT-ATATAAAATATATAAAT
**
1682798 ATATATACAAATATATATTT
1 ATATATA-AAATATATAAAT
1682818 ATATATA
1 ATATATA
1682825 TATATATAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.06
18 14 0.27
19 17 0.33
20 17 0.33
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (19 bp):
ATATATAAAATATATAAAT
Found at i:1685531 original size:2 final size:2
Alignment explanation
Indices: 1685526--1685552 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1685516 AAAAAGCAAA
1685526 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1685553 TTTATCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1685629 original size:56 final size:55
Alignment explanation
Indices: 1685565--1685673 Score: 200
Period size: 56 Copynumber: 2.0 Consensus size: 55
1685555 TATCTTGTTA
1685565 GACAATATTCTAAGCAAAACCCTGAAAAGTTCATGACTTTGATCATGAAAAAAAAC
1 GACAATATTCTAAGCAAAACCCTGAAAAGTTCA-GACTTTGATCATGAAAAAAAAC
*
1685621 GACAATATTCTAAGCAAAACCCTGAAAAGTTCAGACTTTGATCCTGAAAAAAA
1 GACAATATTCTAAGCAAAACCCTGAAAAGTTCAGACTTTGATCATGAAAAAAA
1685674 TTAAACTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 19 0.37
56 33 0.63
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (55 bp):
GACAATATTCTAAGCAAAACCCTGAAAAGTTCAGACTTTGATCATGAAAAAAAAC
Found at i:1686905 original size:2 final size:2
Alignment explanation
Indices: 1686898--1686922 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1686888 TGTTAATAAC
1686898 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1686923 GAAGGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1687624 original size:20 final size:19
Alignment explanation
Indices: 1687599--1687643 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1687589 AGTCTGTTAA
1687599 ATATTATAATTTATATATTT
1 ATATTAT-ATTTATATATTT
* *
1687619 ATATTATATTTGTGTATTT
1 ATATTATATTTATATATTT
1687638 -TATTAT
1 ATATTAT
1687644 GCTATTATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATATTATATTTATATATTT
Found at i:1687869 original size:24 final size:24
Alignment explanation
Indices: 1687819--1687869 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1687809 TTAAGTCAAG
* *
1687819 AATAAAAAATAATTATAAATATGA
1 AATAAAAAATAATTACAAATATAA
*
1687843 AATAAAAAATAATTACAACTATAA
1 AATAAAAAATAATTACAAATATAA
1687867 AAT
1 AAT
1687870 TTAATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
AATAAAAAATAATTACAAATATAA
Found at i:1688703 original size:30 final size:30
Alignment explanation
Indices: 1688667--1688726 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1688657 ACATTCCTAA
1688667 TCTTCTATTCTATTATATCTATAAGATCAC
1 TCTTCTATTCTATTATATCTATAAGATCAC
1688697 TCTTCTATTCTATTATATCTATAAGATCAC
1 TCTTCTATTCTATTATATCTATAAGATCAC
1688727 GTTGCAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (30 bp):
TCTTCTATTCTATTATATCTATAAGATCAC
Found at i:1695940 original size:15 final size:14
Alignment explanation
Indices: 1695906--1695943 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1695896 ATTTATAATT
1695906 AATT-ATAAT-AAA
1 AATTAATAATAAAA
1695918 AATTAATAATAAAA
1 AATTAATAATAAAA
1695932 AATTAAATAATA
1 AATT-AATAATA
1695944 TTATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 7 0.30
15 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTAATAATAAAA
Found at i:1697257 original size:37 final size:38
Alignment explanation
Indices: 1697190--1697264 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 38
1697180 AATATTAAAA
* * *
1697190 AAATTATATTAATATTTATATATATTATAATT-AAATT
1 AAATTAAATTAATATTTATATAAATGATAATTCAAATT
*
1697227 AAATTAAATTAAT-TATTATTTAAATGATAATTCAAATT
1 AAATTAAATTAATAT-TTATATAAATGATAATTCAAATT
1697265 GAAGAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 1 0.03
37 26 0.81
38 5 0.16
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (38 bp):
AAATTAAATTAATATTTATATAAATGATAATTCAAATT
Found at i:1698252 original size:165 final size:163
Alignment explanation
Indices: 1697960--1698260 Score: 408
Period size: 165 Copynumber: 1.8 Consensus size: 163
1697950 TTTTTTTTGC
* * * *
1697960 TTTTTTGAATTAAATTCTTTGCATCATTTACTTAGTCATGTATATAAATAATTATTTCCTTTTGA
1 TTTTTTGAATTAAATTCTTTGCACCATTTACTTAATCATGTATATAAATAATTAATACCTTTTGA
* * * *
1698025 TTGATTTTATAATTTCATTATCTAAAGTTGTTTTAAATTGTCATTTTGTTTTGCAATTTCCATTA
66 TTGACTTAATAATTTCATTATATAAAGTTGTTTTAAATTGCCATTTTGTTTTGCAATTTCCATTA
1698090 AGAAAAAACAAAAATCATTTTCTGAAATTTATAG
131 A-AAAAAACAAAAATCATTTTCTGAAATTTATAG
* * * * *
1698124 TTTTTTGTATTAAGTTTCTTTGCACCATTTGCTTAATCAT-TATGTGAATAATTAATACCTTTTT
1 TTTTTTGAATTAA-ATTCTTTGCACCATTTACTTAATCATGTATATAAATAATTAATACC-TTTT
* * *
1698188 TATTGACTTAATAATTTCATTATATAAAGTTGTTTTTAATTGCCATTTT-TTTTGGCATTTTCCA
64 GATTGACTTAATAATTTCATTATATAAAGTTGTTTTAAATTGCCATTTTGTTTT-GCAATTTCCA
1698252 TTAAAAAAA
128 TTAAAAAAA
1698261 TTCATTAATA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
164 36 0.31
165 82 0.69
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (163 bp):
TTTTTTGAATTAAATTCTTTGCACCATTTACTTAATCATGTATATAAATAATTAATACCTTTTGA
TTGACTTAATAATTTCATTATATAAAGTTGTTTTAAATTGCCATTTTGTTTTGCAATTTCCATTA
AAAAAAACAAAAATCATTTTCTGAAATTTATAG
Found at i:1700134 original size:40 final size:34
Alignment explanation
Indices: 1700090--1700160 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
1700080 AAATTTTTAA
*
1700090 TAATTT-A-AATT-AAATTAATTTTATTTAAATT
1 TAATTTAATAATTAAAAATAATTTTATTTAAATT
*
1700121 ATAATTTAATAATTAAAAATATTTTTATTTAAATT
1 -TAATTTAATAATTAAAAATAATTTTATTTAAATT
1700156 TAATT
1 TAATT
1700161 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 6 0.18
33 1 0.03
34 9 0.26
35 18 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TAATTTAATAATTAAAAATAATTTTATTTAAATT
Found at i:1700143 original size:29 final size:28
Alignment explanation
Indices: 1700111--1700172 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
1700101 AAATTAATTT
1700111 TATTTAAA-TTATAATTTAATAATTAAAAA
1 TATTTAAATTTA-AATTTAATAA-TAAAAA
** *
1700140 TATTTTTATTTAAATTTAATTATAAAAA
1 TATTTAAATTTAAATTTAATAATAAAAA
1700168 TATTT
1 TATTT
1700173 TTTAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 15 0.52
30 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTTAAATTTAAATTTAATAATAAAAA
Found at i:1700148 original size:26 final size:25
Alignment explanation
Indices: 1700119--1700179 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 25
1700109 TTTATTTAAA
1700119 TTATAATTTAATAATTAAAAATATTT
1 TTATAATTTAATAA-TAAAAATATTT
*
1700145 TTATTTAAATTTAATTATAAAAATATTT
1 TTA--T-AATTTAATAATAAAAATATTT
1700173 TT-TAATT
1 TTATAATT
1700180 ATTTTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 4 0.13
25 1 0.03
26 3 0.10
28 14 0.45
29 9 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATAATTTAATAATAAAAATATTT
Found at i:1701614 original size:2 final size:2
Alignment explanation
Indices: 1701607--1701661 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1701597 ACAAATGCAG
1701607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1701649 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1701662 TTCTCATGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1703405 original size:29 final size:29
Alignment explanation
Indices: 1703345--1703405 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1703335 TATAAATAGA
* ***
1703345 TATTGAAATTTATTTTTGTATTTTATTTT
1 TATTGAAATTTATTATTGTATTTTAAAAT
*
1703374 TATTGATATTTATTATTGTATTTTAAAAT
1 TATTGAAATTTATTATTGTATTTTAAAAT
1703403 TAT
1 TAT
1703406 AGGTAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (29 bp):
TATTGAAATTTATTATTGTATTTTAAAAT
Done.