Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2331
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: 26152
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:6409 original size:3 final size:3
Alignment explanation
Indices: 6401--6441 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
6391 GTTATTAACA
6401 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6442 AAGGTAACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9143 original size:2 final size:2
Alignment explanation
Indices: 9138--9163 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9128 ATATATATAT
9138 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
9164 CAATTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9718 original size:9 final size:9
Alignment explanation
Indices: 9706--9735 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9696 AGAAGACGAA
9706 GAAGAAGAG
1 GAAGAAGAG
9715 GAAGAAGAG
1 GAAGAAGAG
*
9724 GAAGAGGAG
1 GAAGAAGAG
9733 GAA
1 GAA
9736 ATTTGGGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (9 bp):
GAAGAAGAG
Found at i:10207 original size:21 final size:22
Alignment explanation
Indices: 10183--10232 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
10173 TTTTTAAGGT
* *
10183 TAATGAAAATGTA-AAATTTTA
1 TAATAAAAATGTATAAATTTAA
*
10204 TAATAAAAATTTATAAATTTAA
1 TAATAAAAATGTATAAATTTAA
10226 TAATAAA
1 TAATAAA
10233 TTTATTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TAATAAAAATGTATAAATTTAA
Found at i:10341 original size:21 final size:20
Alignment explanation
Indices: 10316--10354 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10306 AAAAAATCTA
10316 AAAACATAAAAATCTTAAAGT
1 AAAACATAAAAAT-TTAAAGT
*
10337 AAAACTTAAAAATTTAAA
1 AAAACATAAAAATTTAAA
10355 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAACATAAAAATTTAAAGT
Found at i:11926 original size:27 final size:27
Alignment explanation
Indices: 11885--11955 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
11875 AATTTTATAT
*
11885 ATTTATTAAATTATTATATAAAAATAAA
1 ATTTATTATATTATTATAT-AAAATAAA
11913 ATTTA-TATATTATTATATAAAATAAA
1 ATTTATTATATTATTATATAAAATAAA
*
11939 ATTTATTATATAATTAT
1 ATTTATTATATTATTAT
11956 TTCCATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.32
27 22 0.55
28 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTATTATATTATTATATAAAATAAA
Found at i:11938 original size:32 final size:35
Alignment explanation
Indices: 11865--11939 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 35
11855 TTAATTTCAT
* * *
11865 AATAATAATAAATTTTATATATTTATTAAATTATTA
1 AATAAAAATAAAATTTATATATTTATT-AATTATAA
*
11901 TATAAAAATAAAATTTATATA-TTATT-A-TATAA
1 AATAAAAATAAAATTTATATATTTATTAATTATAA
11933 AATAAAA
1 AATAAAA
11940 TTTATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
32 10 0.29
33 1 0.03
35 5 0.15
36 18 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
AATAAAAATAAAATTTATATATTTATTAATTATAA
Found at i:25672 original size:49 final size:49
Alignment explanation
Indices: 25614--26046 Score: 502
Period size: 49 Copynumber: 8.8 Consensus size: 49
25604 GCAACCCTTC
* *
25614 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
25663 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
25712 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
25761 TAAGACCAATGTAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
25810 TAAGTCCAATATAGCTGGTCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
** *
25858 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
25901 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * *
25953 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCATCTT
* * * * *
26008 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
26047 TCTTTATCAC
Statistics
Matches: 329, Mismatches: 42, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
43 39 0.12
45 1 0.00
48 42 0.13
49 166 0.50
50 1 0.00
52 38 0.12
53 2 0.01
55 39 0.12
56 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:25916 original size:43 final size:43
Alignment explanation
Indices: 25807--25944 Score: 195
Period size: 43 Copynumber: 3.1 Consensus size: 43
25797 GCACCTTCAT
*
25807 CTTTAAGTCCAATATAGCTGGTCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----CAC
**
25855 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
25898 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
25941 CTTT
1 CTTT
25945 TCCATCTTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
43 47 0.56
48 37 0.44
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:25937 original size:91 final size:94
Alignment explanation
Indices: 25807--25997 Score: 289
Period size: 91 Copynumber: 2.0 Consensus size: 94
25797 GCACCTTCAT
*
25807 CTTTAAGTCCAATATAGCTGGTCTTGAATCAGCACATTGGCACC-T-CACCTTTAAGTCCAACGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCCACCTTTAAGTCCAACGT
*
25870 AGCTGGCCTTGAATCAGCACATTGGCA-C
66 AGCTGGCCTTGAATCAGCACATTGACATC
* * * *
25898 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TTCCACCTTTAAGTCCAAC
25963 GTAGCTGGCCTTGAATCAGCACATTGACATC
64 GTAGCTGGCCTTGAATCAGCACATTGACATC
25994 CTTT
1 CTTT
25998 TTCTCATCTT
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
91 42 0.47
94 1 0.01
95 41 0.46
96 5 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (94 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCCACCTTTAAGTCCAACGT
AGCTGGCCTTGAATCAGCACATTGACATC
Found at i:25976 original size:52 final size:53
Alignment explanation
Indices: 25898--26051 Score: 193
Period size: 52 Copynumber: 2.9 Consensus size: 53
25888 ACATTGGCAC
25898 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
25950 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
26005 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
26052 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 36 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Done.