Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2798
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: 31127
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:11112 original size:75 final size:70
Alignment explanation
Indices: 10828--11094 Score: 337
Period size: 70 Copynumber: 3.8 Consensus size: 70
10818 TAAGCCTTTT
* *
10828 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGCTGAGG
10893 TAATTTC
65 T-ATTTC
** *
10900 AATTTC--TTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGT
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGT
10963 ATTTTC
66 A-TTTC
* * * *
10969 AATTTCTG-TTTTCAAAATTAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGCACATGCTGAGG
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-ACACGCTGAGG
11033 TATTTC
65 TATTTC
*
11039 AATTTCTGTTTTTAAAAAAAAATCAACTCATATTGC-AGAGGTGAGTTGAG-CTCAGA
1 AATTTCTGTTTTT----CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
11095 TTACACACTG
Statistics
Matches: 170, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
68 1 0.01
69 22 0.13
70 92 0.54
71 15 0.09
72 6 0.04
73 4 0.02
74 14 0.08
75 16 0.09
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (70 bp):
AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGT
ATTTC
Found at i:11386 original size:71 final size:71
Alignment explanation
Indices: 11247--11386 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 71
11237 TCAAAATCAG
* * * ** *
11247 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTTTTTAA
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATTTAAGCTTTTAA
11312 TTTCAA
66 TTTCAA
* *
11318 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAA-TTAAGCCTTTTG
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATTTAAG-CTTTTA
11382 ATTTC
65 ATTTC
11387 TATTTTCAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 3 0.05
71 57 0.95
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (71 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATTTAAGCTTTTAA
TTTCAA
Found at i:11499 original size:27 final size:25
Alignment explanation
Indices: 11469--11524 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11459 CTGTTTTCAT
*
11469 TATTATGTTTTTGAAAGAATCAACTCA
1 TATTATG-TTTTCAAA-AATCAACTCA
* *
11496 TATTCTGTTTTCAAAATTCAACTCA
1 TATTATGTTTTCAAAAATCAACTCA
11521 TATT
1 TATT
11525 GCGAGAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
26 7 0.27
27 6 0.23
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (25 bp):
TATTATGTTTTCAAAAATCAACTCA
Found at i:11625 original size:73 final size:72
Alignment explanation
Indices: 11498--11694 Score: 315
Period size: 73 Copynumber: 2.7 Consensus size: 72
11488 TCAACTCATA
* *
11498 TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAA
1 TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAA
11563 TTTCAAT
66 TTTCAAT
11570 TTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTA
1 TTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTA
11635 ATTTCAAT
65 ATTTCAAT
* *
11643 TTCTGTTGTCAAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 TTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
11695 TTCACATGTT
Statistics
Matches: 117, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
72 9 0.08
73 73 0.62
74 35 0.30
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (72 bp):
TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAA
TTTCAAT
Found at i:12897 original size:10 final size:9
Alignment explanation
Indices: 12870--12917 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 9
12860 TACATATATT
*
12870 AAAACATAA
1 AAAAAATAA
12879 AAGAAAATACA
1 AA-AAAATA-A
12890 AAAAAAT-A
1 AAAAAATAA
12898 AAAAAATAA
1 AAAAAATAA
12907 AAAAATATAA
1 AAAAA-ATAA
12917 A
1 A
12918 TTTTTACCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 8 0.24
9 8 0.24
10 15 0.44
11 3 0.09
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:12900 original size:8 final size:8
Alignment explanation
Indices: 12889--12913 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12879 AAGAAAATAC
12889 AAAAAAAT
1 AAAAAAAT
12897 AAAAAAAT
1 AAAAAAAT
12905 AAAAAAAT
1 AAAAAAAT
12913 A
1 A
12914 TAAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12905 original size:18 final size:18
Alignment explanation
Indices: 12882--12917 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12872 AACATAAAAG
12882 AAAATACAAAAAA-ATAAA
1 AAAATA-AAAAAATATAAA
12900 AAAATAAAAAAATATAAA
1 AAAATAAAAAAATATAAA
12918 TTTTTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAATAAAAAAATATAAA
Found at i:13036 original size:11 final size:11
Alignment explanation
Indices: 13020--13059 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
13010 CCCTTCCCCC
13020 CTCCCTTCTCT
1 CTCCCTTCTCT
13031 CTCCCTTCTCT
1 CTCCCTTCTCT
13042 CTTCCC-TCTCT
1 C-TCCCTTCTCT
*
13053 CTTCCTT
1 CTCCCTT
13060 TTTTCTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 19 0.73
12 4 0.15
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:13054 original size:22 final size:23
Alignment explanation
Indices: 13021--13074 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
13011 CCTTCCCCCC
13021 TCCCTTCTCTCTCCCTTCTCTC-T
1 TCCC-TCTCTCTCCCTTCTCTCTT
* * *
13044 TCCCTCTCTCTTCCTTTTTTCTT
1 TCCCTCTCTCTCCCTTCTCTCTT
13067 TCCCTCTC
1 TCCCTCTC
13075 CCCAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (23 bp):
TCCCTCTCTCTCCCTTCTCTCTT
Found at i:13540 original size:3 final size:3
Alignment explanation
Indices: 13532--13568 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
13522 TGTATTTCAA
13532 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13569 GTACATTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13724 original size:127 final size:129
Alignment explanation
Indices: 13541--13778 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 129
13531 ATATTATTAT
* * * * *
13541 TATTATTATTATTATTATTATTATTATTGTACATTAGTGTATATTTTCATGTATGTATATATATA
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATATTTTCATGTATGTATATATACA
* * *
13606 TGTAGTAATGTTTTT-ATTACTTTATTTTAATAT-TTTTTATTATAATAGCTTTTGTATTTCAA
66 TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
*
13668 TATTATTATTATTTTTATTATTATCATT-AACATTACTATATATTCTT-AT-TAGATGTATATAT
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATATT-TTCATGT--ATGTATATAT
* *
13730 ACATATATTACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
63 ACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
13779 TTTACTTTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
125 1 0.01
126 15 0.16
127 52 0.55
128 17 0.18
129 10 0.11
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (129 bp):
TATTATTATTATTATTATTATTATCATTGAACATTACTATATATTTTCATGTATGTATATATACA
TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
Found at i:16448 original size:18 final size:19
Alignment explanation
Indices: 16427--16462 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16417 TTTTTTTATT
16427 ATTAATA-ATTTTAAAATA
1 ATTAATATATTTTAAAATA
*
16445 ATTAATATTTTTTAAAAT
1 ATTAATATATTTTAAAAT
16463 TTAGAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAATATATTTTAAAATA
Found at i:19164 original size:13 final size:13
Alignment explanation
Indices: 19146--19174 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19136 TGTATAATTA
19146 TATTATAATTTTC
1 TATTATAATTTTC
19159 TATTATAATTTTC
1 TATTATAATTTTC
19172 TAT
1 TAT
19175 GTGAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATAATTTTC
Found at i:25143 original size:40 final size:40
Alignment explanation
Indices: 25011--25146 Score: 168
Period size: 40 Copynumber: 3.4 Consensus size: 40
25001 GACTATGCTT
*** * *
25011 GGCACTAAGTGTGCG-GTTTAATATAGCTTCGGCTACA-AA
1 GGCACTAAGTGTGCGAG-TTGGCATAGCTTCAGCTATATAA
** *
25050 TGGCACTAAGTGTATGAGTTGGCGTAGCTTCAGCTATATAA
1 -GGCACTAAGTGTGCGAGTTGGCATAGCTTCAGCTATATAA
25091 GGCACTAAGTGTGCGAGTTGGCATAGCTTCAGCTATATAA
1 GGCACTAAGTGTGCGAGTTGGCATAGCTTCAGCTATATAA
25131 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
25147 TACCGACTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 80 0.96
41 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (40 bp):
GGCACTAAGTGTGCGAGTTGGCATAGCTTCAGCTATATAA
Found at i:28026 original size:39 final size:40
Alignment explanation
Indices: 27981--28148 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
27971 CGGGGTTTAG
* * *
27981 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
28020 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
28060 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
28100 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
28141 CCGGATAT
1 CCGGATAT
28149 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:28131 original size:41 final size:40
Alignment explanation
Indices: 28004--28148 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
27994 CTCGCACAAG
* * * * *
28004 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
28044 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
28084 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
28125 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
28149 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Done.