Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2265
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: 44183
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:53 original size:40 final size:40
Alignment explanation
Indices: 6--126 Score: 148
Period size: 37 Copynumber: 3.1 Consensus size: 40
1 GCTAA
*
6 CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAG-TACTATAATCCGGGCTAAGTC
46 CCGAAGGCA-TTGTGCG-G-ACTATAATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTACTATAATCCGGGCTAAGTC
* *
83 CCGAAGGCATTTGAGCGAGTAGCTAT-ATCC-GGCTAAAT-
1 CCGAAGGCATTTGTGCGAGTA-CTATAATCCGGGCTAAGTC
121 CCGAAG
1 CCGAAG
127 TACTTGGGTT
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
36 4 0.05
37 23 0.32
38 13 0.18
39 15 0.21
40 14 0.19
41 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTACTATAATCCGGGCTAAGTC
Found at i:8295 original size:40 final size:40
Alignment explanation
Indices: 8223--8492 Score: 393
Period size: 40 Copynumber: 6.8 Consensus size: 40
8213 TGGATCATAA
* *
8223 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
* *
8263 CGAAGGCATTTGTGGGAGTTACTATATTCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* **
8303 CGAAGGAATTTGTGCGAGTTACTATATCCAAGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
8343 CAAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
8383 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
8423 CGAAGGCATTTGTGCGAGTTACTATAACCGGGCT-AGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
8462 CAAAGACATTTGAGCGAG-TAGCTATATCCGG
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGG
8493 TTAAATCTCG
Statistics
Matches: 209, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
38 2 0.01
39 29 0.14
40 177 0.85
41 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:11034 original size:27 final size:27
Alignment explanation
Indices: 10997--11127 Score: 172
Period size: 27 Copynumber: 4.9 Consensus size: 27
10987 ATTACCAAAG
* * *
10997 TACCCTGGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* **
11024 TACTCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
11051 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
11078 TACCCTTGATTTACATAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
11105 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
11128 AAAATACCCT
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:11135 original size:27 final size:27
Alignment explanation
Indices: 11105--11352 Score: 166
Period size: 27 Copynumber: 9.2 Consensus size: 27
11095 ATTACTGTTT
* *
11105 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
11132 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * * * *
11159 TACCCTAG-TCTGTAAAATTGCTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
11185 TACCC-CTGGTTTGTAAAATTACCGAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * *
11212 TATCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
11239 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* * * * *
11266 TACCACT-GGTTTGTGAAATTATCGAAA
1 TACC-CTCGATTTATAAAATTACCAAAA
* * *
11293 TACCCTCAAATTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
11320 TACCC-CTGATTTACAAAGTTACAAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
11347 TACCCT
1 TACCCT
11353 TGACTTTTTA
Statistics
Matches: 173, Mismatches: 37, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
26 25 0.14
27 146 0.84
28 2 0.01
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:11163 original size:54 final size:55
Alignment explanation
Indices: 11105--11352 Score: 208
Period size: 54 Copynumber: 4.6 Consensus size: 55
11095 ATTACTGTTT
** **
11105 TACCCTCGATTTACAAAATTACTAAAATACCCTC-GATCAGTAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACTAAAATACCCTCAGATTTGTAAAATTACCAAAA
* * * * * *
11159 TACCCTAG-TCTGTAAAATTGCTAAAATACCC-CTGGTTTGTAAAATTACCGAAA
1 TACCCTCGATTTGTAAAATTACTAAAATACCCTCAGATTTGTAAAATTACCAAAA
* * *
11212 TATCCTCAATTTGTAAAATTACCAAAATACCC-CTAG-TTTGTAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACTAAAATACCCTC-AGATTTGTAAAATTACCAAAA
* * * *
11266 TACCACT-GGTTTGTGAAATTA-TCGAAATACCCTCA-AATTGTAAAATTACCAAAA
1 TACC-CTCGATTTGTAAAATTACT-AAAATACCCTCAGATTTGTAAAATTACCAAAA
** * *
11320 TACCC-CTGATTTACAAAGTTACAAAAATACCCT
1 TACCCTC-GATTTGTAAAATTACTAAAATACCCT
11353 TGACTTTTTA
Statistics
Matches: 153, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
52 1 0.01
53 41 0.27
54 107 0.70
55 4 0.03
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (55 bp):
TACCCTCGATTTGTAAAATTACTAAAATACCCTCAGATTTGTAAAATTACCAAAA
Found at i:11163 original size:81 final size:80
Alignment explanation
Indices: 10952--11164 Score: 194
Period size: 81 Copynumber: 2.6 Consensus size: 80
10942 AATACTTTAG
* * * * * *
10952 TTTACCAAATTACTAAAATGCCCTCAAATTGTAAAATTACCAAAGTACCCTGGATTTATAGAATT
1 TTTACAAAATTACTAAAATACCCTC-GATAGTAAAATTACCAAAATACCCTGGATTTACAGAATT
* *
11017 ATTGTTTTACTCTCGA
65 ACTGTTTTACCCTCGA
* * *** * ***** * *
11033 TTTACAGAATTACCATTTTACCCTCGATTTA-TAGAATTACTGTTTTACCCTTGATTTACATAAT
1 TTTACAAAATTACTAAAATACCCTCGA--TAGTAAAATTACCAAAATACCCTGGATTTACAGAAT
11097 TACTGTTTTACCCTCGA
64 TACTGTTTTACCCTCGA
11114 TTTACAAAATTACTAAAATACCCTCGATCAGTAAAATTACCAAAATACCCT
1 TTTACAAAATTACTAAAATACCCTCGAT-AGTAAAATTACCAAAATACCCT
11165 AGTCTGTAAA
Statistics
Matches: 97, Mismatches: 31, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
79 1 0.01
80 2 0.02
81 93 0.96
82 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (80 bp):
TTTACAAAATTACTAAAATACCCTCGATAGTAAAATTACCAAAATACCCTGGATTTACAGAATTA
CTGTTTTACCCTCGA
Found at i:11279 original size:81 final size:81
Alignment explanation
Indices: 11144--11326 Score: 287
Period size: 81 Copynumber: 2.3 Consensus size: 81
11134 CCCTCGATCA
* * *
11144 GTAAAATTACCAAAATA-CCCTAGTCTGTAAAATTGCTAAAATACCCCTGGTTTGTAAAATTACC
1 GTAAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTACC
* *
11208 GAAATATCCTCAATTT
66 GAAATACCCTCAAATT
* * *
11224 GTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTATC
1 GTAAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTACC
11289 GAAATACCCTCAAATT
66 GAAATACCCTCAAATT
11305 GTAAAATTACCAAAATACCCCT
1 GTAAAATTACCAAAATACCCCT
11327 GATTTACAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 17 0.18
81 77 0.82
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (81 bp):
GTAAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTACC
GAAATACCCTCAAATT
Found at i:11347 original size:81 final size:80
Alignment explanation
Indices: 11144--11350 Score: 267
Period size: 81 Copynumber: 2.6 Consensus size: 80
11134 CCCTCGATCA
* * *
11144 GTAAAATTACCAAAATA-CCCT-AGTCTGTAAAATTGCTAAAATACCCCTGGTTTGTAAAATTAC
1 GTAAAATTACCAAAATACCCCTGA-T-TGTAAAATTACAAAAATACCACTGGTTTGTAAAATTAC
* *
11207 CGAAATATCCTCAATTT
64 CGAAATACCCTCAAATT
* * * *
11224 GTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTATC
1 GTAAAATTACCAAAATACCCCT-GATTGTAAAATTACAAAAATACCACTGGTTTGTAAAATTACC
11289 GAAATACCCTCAAATT
65 GAAATACCCTCAAATT
11305 GTAAAATTACCAAAATACCCCTGATT-TACAAAGTTACAAAAATACC
1 GTAAAATTACCAAAATACCCCTGATTGTA-AAA-TTACAAAAATACC
11351 CTTGACTTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
79 2 0.02
80 23 0.21
81 86 0.77
82 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (80 bp):
GTAAAATTACCAAAATACCCCTGATTGTAAAATTACAAAAATACCACTGGTTTGTAAAATTACCG
AAATACCCTCAAATT
Found at i:12291 original size:16 final size:16
Alignment explanation
Indices: 12270--12300 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12260 CAAATATGGG
*
12270 CATGACATTTTGCATA
1 CATGACATGTTGCATA
12286 CATGACATGTTGCAT
1 CATGACATGTTGCAT
12301 TGGGTTGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:12380 original size:25 final size:25
Alignment explanation
Indices: 12346--12416 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
12336 AAGGGCTTAC
*
12346 GCCCTAGTTTATTGAAAAAGGCTTT
1 GCCCAAGTTTATTGAAAAAGGCTTT
** *
12371 GCCCAAGTTTACCGAAAAGGGCTTT
1 GCCCAAGTTTATTGAAAAAGGCTTT
* *
12396 GCCCCAG-TTATT-AAAGAGGCT
1 GCCCAAGTTTATTGAAAAAGGCT
12417 AGGCCTCCAG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 7 0.19
24 3 0.08
25 27 0.73
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (25 bp):
GCCCAAGTTTATTGAAAAAGGCTTT
Found at i:12608 original size:42 final size:42
Alignment explanation
Indices: 12549--12640 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
12539 TAGTCTCCCC
* ** *
12549 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
12591 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
12633 AAATGGGC
1 AAATGGGC
12641 CTAAGGGTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:12715 original size:31 final size:31
Alignment explanation
Indices: 12664--12740 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
12654 TGTTTACAGT
*
12664 AAAGGCTTCGGTCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
12695 AAATGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
*
12726 AAAGGCTTCAGCCCA
1 AAAGGCTTCGGCCCA
12741 TTAACTGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:18530 original size:29 final size:28
Alignment explanation
Indices: 18464--18603 Score: 117
Period size: 29 Copynumber: 4.9 Consensus size: 28
18454 TACATACCTG
18464 CATATGGCCCA-CTAGGCCCAATCTCA-TT
1 CATATGGCCCATCT-GGCCCAAT-TCACTT
* *
18492 TATATGGCCCATCTGGTCCAATTCACGTT
1 CATATGGCCCATCTGGCCCAATTCAC-TT
* *
18521 CATATGGCCCATCAGGCCCAACTCACATT
1 CATATGGCCCATCTGGCCCAATTCAC-TT
**
18550 CATATGGCCCAT-TAGGCCTGATCTCA-TT
1 CATATGGCCCATCT-GGCCCAAT-TCACTT
* * *
18578 TATATGGCCCATCCGGCCCAAATCAC
1 CATATGGCCCATCTGGCCCAATTCAC
18604 ATTATACTCA
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
27 6 0.07
28 35 0.39
29 45 0.51
30 3 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (28 bp):
CATATGGCCCATCTGGCCCAATTCACTT
Found at i:18595 original size:28 final size:27
Alignment explanation
Indices: 18464--18595 Score: 115
Period size: 28 Copynumber: 4.7 Consensus size: 27
18454 TACATACCTG
18464 CATATGGCCCA-CTAGGCCCAATCTCATT
1 CATATGGCCCATC-AGG-CCAATCTCATT
* *
18492 TATATGGCCCATCTGGTCCAAT-TCACGTT
1 CATATGGCCCATCAGG-CCAATCTCA--TT
*
18521 CATATGGCCCATCAGGCCCAACTCACATT
1 CATATGGCCCATCAGG-CCAA-TCTCATT
* *
18550 CATATGGCCCATTAGGCCTGATCTCATT
1 CATATGGCCCATCAGGCC-AATCTCATT
* *
18578 TATATGGCCCATCCGGCC
1 CATATGGCCCATCAGGCC
18596 CAAATCACAT
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.04
28 40 0.47
29 39 0.46
30 1 0.01
31 2 0.02
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (27 bp):
CATATGGCCCATCAGGCCAATCTCATT
Found at i:18828 original size:16 final size:16
Alignment explanation
Indices: 18807--18849 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
18797 CGTAGCCAAA
18807 ATTTTGACTTTTCGGC
1 ATTTTGACTTTTCGGC
*
18823 ATTTTGACTTTTTGGC
1 ATTTTGACTTTTCGGC
*
18839 ATTTTGGCTTT
1 ATTTTGACTTT
18850 CGCTGATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.56
Consensus pattern (16 bp):
ATTTTGACTTTTCGGC
Found at i:36863 original size:27 final size:27
Alignment explanation
Indices: 36828--37032 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
36818 TAAATTGTAC
36828 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
36855 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
36882 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
36908 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
36936 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
36964 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
36991 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
37018 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
37033 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:36967 original size:109 final size:108
Alignment explanation
Indices: 36829--37032 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
36819 AAATTGTACA
* *
36829 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
36894 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
36937 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
37002 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
37033 GACTCAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 17 0.20
109 70 0.80
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Done.