Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1660
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: 9735
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Found at i:97 original size:53 final size:53
Alignment explanation
Indices: 1--543 Score: 246
Period size: 56 Copynumber: 9.8 Consensus size: 53
* *
1 TAAAGCCCACACAAGTTGGTGGCATTTTCCAGT-CTCAAAGAGCAGGACACATCT
1 TAAAGCCCACACAAG-TGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACACCTCT
* * *
55 TAAAGCCCACACAAGTGGT-GCACTTCCTAATCCTCAAAGAGCAGGATACCTTT
1 TAAAGCCCACACAAGTGGTGGCACTTCC-AGTCCTCAAAGAGCAGGACACCTCT
*
108 TAAAGCCCACACACAATTGGTGGCACTTTTCC-GTCCTCAAAGAGCA-GACACTTCGCTCTT
1 TAAAG-CC-CACACAAGTGGTGGCAC--TTCCAGTCCTCAAAGAGCAGGACA---C-CTC-T
* * * * *
168 TCAAAGCCCACACAAGTTGTGGCATTTCCAATTCTCAAAGA-CAGGATACCT-T
1 T-AAAGCCCACACAAGTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACACCTCT
* * *** *
220 TAAAGCCCACCCAATTGGTGGCAC-T-CAGTCCTCAAAGAGCAGAGTATTTTTCTTT
1 TAAAGCCCACACAAGTGGTGGCACTTCCAGTCCTCAAAGAGCAG-G-A--CACCTCT
* * *
275 TCAAAGCCCACACAAGTTGTTGGCATTTTCCATGTCC-CAAAAGAGCAGGACGGCCTTTTCTTT
1 T-AAAGCCCACACAAG-TGGTGGCA-CTTCCA-GTCCTC-AAAGAGCAGGAC-ACC---TC--T
* * **
338 TAAAAAGCCCACACAAGTTGT-GTACCTT-CAGTCCTC-AAGAGCAGGATGCCTTTTTCTT
1 T--AAAGCCCACACAAGTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACACC----TC-T
* * *
396 TCAA-CCC-CACAAGTTGGTGGCATTTCCAATCC-CAAA-AGGCAGGACACCT-T
1 TAAAGCCCACACAAG-TGGTGGCACTTCCAGTCCTCAAAGA-GCAGGACACCTCT
* *
446 TCAAAGCCGCACACAAGGTTGGTGGTCATTTTCAGTCCTC-AAGAGCAGGACA-CT-T
1 T-AAAGCC-CACACAA-G-TGGTGG-CACTTCCAGTCCTCAAAGAGCAGGACACCTCT
**
501 TCAAAG-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAG
1 T-AAAGCCCACACAAG-TGGTGGCA-CTTCCAGTCCTCAAAGAG
544 TTAGGACGCT
Statistics
Matches: 387, Mismatches: 50, Indels: 105
0.71 0.09 0.19
Matches are distributed among these distances:
49 11 0.03
50 6 0.02
51 28 0.07
52 29 0.07
53 40 0.10
54 34 0.09
55 44 0.11
56 68 0.18
57 15 0.04
58 24 0.06
59 33 0.09
60 12 0.03
61 21 0.05
62 4 0.01
63 4 0.01
64 14 0.04
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (53 bp):
TAAAGCCCACACAAGTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACACCTCT
Found at i:279 original size:107 final size:113
Alignment explanation
Indices: 1--302 Score: 330
Period size: 107 Copynumber: 2.8 Consensus size: 113
* * *
1 TAAAGCCCACACA-AGTTGGTGGCATTTTCCAGT-CTCAAAGAGCAGGACA---C-ATC-TT-AA
1 TAAAGCCCACACACAATTGGTGGCA-CTT-CAGTCCTCAAAGAGCA-GACACTTCGCTCTTTCAA
* *
58 AGCCCACACAAGTGGT-GCACTTCCTAATCCTCAAAGAGCAGGATACCTTT
63 AGCCCACACAAGTTGTGGCATTTCCTAATCCTCAAAGAGCAGGATACCTTT
*
108 TAAAGCCCACACACAATTGGTGGCACTTTTCCGTCCTCAAAGAGCAGACACTTCGCTCTTTCAAA
1 TAAAGCCCACACACAATTGGTGGCAC--TTCAGTCCTCAAAGAGCAGACACTTCGCTCTTTCAAA
*
173 GCCCACACAAGTTGTGGCATTTCC-AATTCTCAAAGA-CAGGATACC-TT
64 GCCCACACAAGTTGTGGCATTTCCTAATCCTCAAAGAGCAGGATACCTTT
* * **
220 TAAAGCCCAC-C-CAATTGGTGGCAC-TCAGTCCTCAAAGAGCAGAGTATTTTTCT-TTTCAAAG
1 TAAAGCCCACACACAATTGGTGGCACTTCAGTCCTCAAAGAGCAGA-CACTTCGCTCTTTCAAAG
281 CCCACACAAGTTGTTGGCATTT
65 CCCACACAAGTTG-TGGCATTT
303 TCCATGTCCC
Statistics
Matches: 170, Mismatches: 12, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
107 52 0.31
108 30 0.18
109 13 0.08
110 13 0.08
111 2 0.01
112 14 0.08
113 11 0.06
114 28 0.16
115 7 0.04
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (113 bp):
TAAAGCCCACACACAATTGGTGGCACTTCAGTCCTCAAAGAGCAGACACTTCGCTCTTTCAAAGC
CCACACAAGTTGTGGCATTTCCTAATCCTCAAAGAGCAGGATACCTTT
Found at i:283 original size:168 final size:167
Alignment explanation
Indices: 2--322 Score: 390
Period size: 168 Copynumber: 1.9 Consensus size: 167
1 T
2 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTCAAAGAGCAGGACACATCTTAAAGCCCACAC
1 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTCAAAGAGCAGGACACATCTTAAAGCCCACAC
67 AAGTGGTGCACTTCCTAATCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACACAATTGGTGGC
66 AAGTGGTGCACTTCCTAATCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACA-AATTGGTGGC
132 ACTTTTCC-GTCCTC-AAAGAGCAGACACTTCGCTCTTTC
130 A-TTTTCCAGTCC-CAAAAGAGCAGACACTTCGCTCTTTC
* * * *
170 AAAGCCCACACAAGTT-GTGGCA-TTTCCAATTCTCAAAGA-CAGGATACCT-TTAAAGCCCACC
1 AAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCTCAAAGAGCAGGACACATCTTAAAGCCCACA
* * ** *
231 CAATTGGTGGCAC-T-C-AGTCCTCAAAGAGCAGAGTATTTTTCTTTTCAAAGCCCACACAAGTT
65 CAAGTGGT-GCACTTCCTAATCCTCAAAGAGCAG-G-A--TACCTTTT-AAAGCCCACACAAATT
*
293 GTTGGCATTTTCCATGTCCCAAAAGAGCAG
124 GGTGGCATTTTCCA-GTCCCAAAAGAGCAG
323 GACGGCCTTT
Statistics
Matches: 133, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
163 15 0.11
164 2 0.02
165 20 0.15
166 23 0.17
167 32 0.24
168 41 0.31
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (167 bp):
AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTCAAAGAGCAGGACACATCTTAAAGCCCACAC
AAGTGGTGCACTTCCTAATCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACAAATTGGTGGCA
TTTTCCAGTCCCAAAAGAGCAGACACTTCGCTCTTTC
Found at i:503 original size:55 final size:51
Alignment explanation
Indices: 403--569 Score: 169
Period size: 54 Copynumber: 3.1 Consensus size: 51
393 CTTTCAACCC
* * *
403 CACAAGTTGGTGGCATTTCCAATCC-CAAAAGGCAGGACACCTTTCAAAGCCGCA
1 CACAAGTTGGTGGCATTTTCAGTCCTCAAGA-GCAGGACA-CTTTCAAAG-C-CA
457 CACAAGGTTGGTGGTCATTTTCAGTCCTCAAGAGCAGGACACTTTCAAAGCCA
1 CACAA-GTTGGTGG-CATTTTCAGTCCTCAAGAGCAGGACACTTTCAAAGCCA
* *
510 CACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGTTAGGACGCTTTCAAAGGCC-
1 CACAAGTTGGTGGCA--TTTTCAGTCCTC-AAGAG-CAGGACACTTTCAAA-GCCA
564 CACAAG
1 CACAAG
570 GACGAGTTGG
Statistics
Matches: 100, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
51 2 0.02
52 15 0.15
53 16 0.16
54 25 0.25
55 20 0.20
56 18 0.18
57 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (51 bp):
CACAAGTTGGTGGCATTTTCAGTCCTCAAGAGCAGGACACTTTCAAAGCCA
Found at i:3858 original size:28 final size:29
Alignment explanation
Indices: 3821--3876 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
3811 GTTAATCATC
*
3821 GGGGATACTCTAACCCCG-TTATTTCCGA
1 GGGGATACTCCAACCCCGCTTATTTCCGA
3849 GGGGATACTCCAACCCCGCTTTATTTCC
1 GGGGATACTCCAACCCCGC-TTATTTCC
3877 AAATATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 17 0.68
30 8 0.32
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.29
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGCTTATTTCCGA
Found at i:3875 original size:30 final size:28
Alignment explanation
Indices: 3794--3876 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
3784 CTTCACAATC
* * ***
3794 GGGGACACTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
*
3821 GGGGATACTCTAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
3849 GGGGATACTCCAACCCCGCTTTATTTCC
1 GGGGATACTCCAACCCCG--TTATTTCC
3877 AAATATTGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 19 0.41
28 19 0.41
30 8 0.17
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Done.