Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold12557.1
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: 2175
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Found at i:825 original size:30 final size:29
Alignment explanation
Indices: 780--866 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
770 GTTTCTTTTG
*
780 TTTCAATTTCTTTTTCATCTTCTTTTTCAC
1 TTTCAATTTCTTTTTCAT-TTCTTTTTCAA
*
810 TTTCAAATTTC-TTTTCGTTCTCTTTTTCAA
1 TTTC-AATTTCTTTTTCATT-TCTTTTTCAA
* *
840 TCTCATTTTCTTTTTCATTTTCTTTTT
1 TTTCAATTTCTTTTTCA-TTTCTTTTT
867 GCTTTTCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 6 0.12
30 34 0.71
31 8 0.17
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTCAATTTCTTTTTCATTTCTTTTTCAA
Found at i:866 original size:18 final size:18
Alignment explanation
Indices: 817--872 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
807 CACTTTCAAA
* *
817 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
834 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
852 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
871 TT
1 TT
873 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:873 original size:12 final size:12
Alignment explanation
Indices: 780--866 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
770 GTTTCTTTTG
*
780 TTTCAATTTCTT
1 TTTCATTTTCTT
*
792 TTTCATCTTCTT
1 TTTCATTTTCTT
* **
804 TTTCACTTTCAAA
1 TTTCATTTTC-TT
*
817 TTTC-TTTTCGT
1 TTTCATTTTCTT
* * **
828 TCTCTTTTTCAA
1 TTTCATTTTCTT
*
840 TCTCATTTTCTT
1 TTTCATTTTCTT
852 TTTCATTTTCTT
1 TTTCATTTTCTT
864 TTT
1 TTT
867 GCTTTTCAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
11 3 0.05
12 50 0.88
13 4 0.07
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.66
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:884 original size:12 final size:12
Alignment explanation
Indices: 869--899 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
859 TTCTTTTTGC
869 TTTTCAAAGGCT
1 TTTTCAAAGGCT
881 TTTTCAAAGGCT
1 TTTTCAAAGGCT
893 TTTTCAA
1 TTTTCAA
900 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:980 original size:15 final size:14
Alignment explanation
Indices: 940--985 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
930 TACTTGCCTC
*
940 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
955 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
970 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
985 T
1 T
986 TCCTTTCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:996 original size:16 final size:16
Alignment explanation
Indices: 941--996 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
931 ACTTGCCTCT
*
941 CTTTTCTTTTTATTTC
1 CTTTTCTTTTTCTTTC
*
957 ATTTTCTTTTTC-TT-
1 CTTTTCTTTTTCTTTC
971 CTTTTGCTTTTTCTTTC
1 CTTTT-CTTTTTCTTTC
*
988 CTTTCCTTT
1 CTTTTCTTT
997 ATTTTCTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 16 0.48
17 4 0.12
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (16 bp):
CTTTTCTTTTTCTTTC
Found at i:1943 original size:12 final size:12
Alignment explanation
Indices: 1923--1970 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
1913 TTCAGATTTT
1923 TTTTCTTTTCGAAA
1 TTTT-TTTT-GAAA
*
1937 TTTTTTTTTGAAT
1 -TTTTTTTTGAAA
1950 TTTTTTTTG-AA
1 TTTTTTTTGAAA
1961 TTTTTTTTGA
1 TTTTTTTTGA
1971 CTTGTATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 9 0.30
13 3 0.10
14 4 0.13
15 4 0.13
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGAAA
Found at i:1970 original size:11 final size:12
Alignment explanation
Indices: 1935--1968 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1925 TTCTTTTCGA
1935 AATTTTTTTTTG
1 AATTTTTTTTTG
1947 AATTTTTTTTTG
1 AATTTTTTTTTG
1959 AATTTTTTTT
1 AATTTTTTTT
1969 GACTTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Done.