Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2049
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: 29304
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:3659 original size:26 final size:27
Alignment explanation
Indices: 3597--3664 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
3587 TATATGAGTC
* *
3597 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
3624 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
3650 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3665 GTACATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 16 0.42
27 22 0.58
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:5951 original size:15 final size:14
Alignment explanation
Indices: 5927--5956 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5917 CTGTCACATA
5927 TTTATATTTTTTTC
1 TTTATATTTTTTTC
5941 TTTATTATTTTTTTC
1 TTTA-TATTTTTTTC
5956 T
1 T
5957 AACATCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATATTTTTTTC
Found at i:6688 original size:47 final size:47
Alignment explanation
Indices: 6610--6714 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
6600 GAGTGTCATG
* *
6610 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAA-AAATC
* *
6657 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
6705 GAAAAAGAAA
1 GAAAAAGAAA
6715 GAAAACAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:8423 original size:20 final size:20
Alignment explanation
Indices: 8377--8423 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
8367 AGCTCGTTTC
*
8377 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
8397 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
8417 CAGCTCA
1 CAGCTCA
8424 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:9905 original size:24 final size:23
Alignment explanation
Indices: 9878--9943 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 23
9868 AATTTGAAGG
9878 ATGTATAATGCTTTCCTTTAAATA
1 ATGTATAATGC-TTCCTTTAAATA
* * *
9902 ATGTA-ACA-AC-TCCTTTGAATT
1 ATGTATA-ATGCTTCCTTTAAATA
9923 ATGTATAATGCTCTCCTTTAA
1 ATGTATAATGCT-TCCTTTAA
9944 TTGATGTAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
21 15 0.47
22 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (23 bp):
ATGTATAATGCTTCCTTTAAATA
Found at i:9961 original size:21 final size:20
Alignment explanation
Indices: 9891--9961 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 20
9881 TATAATGCTT
* *
9891 TCCTTTAAATAATGTAACAAC
1 TCCTTT-AATTATGTAACAGC
9912 TCCTTTGAATTATGTATA-ATGCTC
1 TCCTTT-AATTATGTA-ACA-G--C
9936 TCCTTTAATTGATGTAACAGC
1 TCCTTTAATT-ATGTAACAGC
9957 TCCTT
1 TCCTT
9962 GTATGTAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 21 0.51
22 1 0.02
23 6 0.15
24 13 0.32
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
TCCTTTAATTATGTAACAGC
Found at i:10312 original size:19 final size:19
Alignment explanation
Indices: 10288--10326 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
10278 TTATTCCAGC
10288 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
10307 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
10326 A
1 A
10327 GTAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:11748 original size:20 final size:20
Alignment explanation
Indices: 11708--11748 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11698 GTCTTAGCCG
*
11708 AATTAAATGTGTCCTAGTTT
1 AATTAAATGTGTCCTAATTT
* *
11728 AATTAAATTTGTCTTAATTT
1 AATTAAATGTGTCCTAATTT
11748 A
1 A
11749 TTACATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (20 bp):
AATTAAATGTGTCCTAATTT
Found at i:14023 original size:27 final size:27
Alignment explanation
Indices: 13989--14166 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
13979 TAAATTGTAC
13989 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
14016 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
14042 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
14070 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
14098 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
14125 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
14152 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
14167 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:14103 original size:82 final size:81
Alignment explanation
Indices: 13990--14145 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
13980 AAATTGTACA
* *
13990 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
14054 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
14071 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
14136 TGCGAGTTGA
65 TGCGAATTGA
14146 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:14157 original size:82 final size:81
Alignment explanation
Indices: 13986--14166 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
13976 GGTTAAATTG
* *
13986 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
14051 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
14067 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
14131 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
14149 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
14167 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21836 original size:27 final size:27
Alignment explanation
Indices: 21805--21982 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21795 TAAATTGTAC
21805 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21832 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21858 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21886 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21914 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21941 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21968 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21983 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21925 original size:82 final size:81
Alignment explanation
Indices: 21806--21961 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21796 AAATTGTACA
* *
21806 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21870 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21887 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21952 TGCGAGTTGA
65 TGCGAATTGA
21962 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21973 original size:82 final size:81
Alignment explanation
Indices: 21802--21982 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
21792 GGTTAAATTG
* *
21802 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
21867 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
21883 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21947 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21965 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21983 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:24893 original size:22 final size:22
Alignment explanation
Indices: 24845--24893 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
24835 TCATCAATGG
*
24845 AAAATTGGAAAAAGAAAATGAT
1 AAAATTGGAAAAAGAAAATAAT
* ** *
24867 TAAATTGGAAAGTGGAAATAAT
1 AAAATTGGAAAAAGAAAATAAT
24889 AAAAT
1 AAAAT
24894 ATGATAAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.22
Consensus pattern (22 bp):
AAAATTGGAAAAAGAAAATAAT
Found at i:25303 original size:20 final size:20
Alignment explanation
Indices: 25245--25295 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
25235 TGTAAAGATG
25245 TAAAATTTATGGAAAAATTA
1 TAAAATTTATGGAAAAATTA
25265 TAAAATTTATGGAAAAATTA
1 TAAAATTTATGGAAAAATTA
25285 TAAAATTTATG
1 TAAAATTTATG
25296 AATTAATTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (20 bp):
TAAAATTTATGGAAAAATTA
Found at i:25452 original size:5 final size:5
Alignment explanation
Indices: 25442--25491 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
25432 TCCTAGGATG
* *
25442 TGAAT TGAAT TGAAT TGAAT ATGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
25492 TCTAAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 29 0.74
6 10 0.26
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (5 bp):
TGAAT
Found at i:25468 original size:11 final size:11
Alignment explanation
Indices: 25442--25480 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
25432 TCCTAGGATG
25442 TGAATTGAAT-
1 TGAATTGAATA
25452 TGAATTGAATA
1 TGAATTGAATA
25463 TGAATTGAATA
1 TGAATTGAATA
25474 TGAATTG
1 TGAATTG
25481 TATTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:25468 original size:16 final size:15
Alignment explanation
Indices: 25442--25491 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
25432 TCCTAGGATG
25442 TGAATTGAATTGAAT
1 TGAATTGAATTGAAT
25457 TGAATATGAATTGAAT
1 TGAAT-TGAATTGAAT
* *
25473 ATGAATTGTATTAAAT
1 -TGAATTGAATTGAAT
25489 TGA
1 TGA
25492 TCTAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.26
16 18 0.58
17 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (15 bp):
TGAATTGAATTGAAT
Found at i:26008 original size:26 final size:26
Alignment explanation
Indices: 25944--26010 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
25934 TGAGTGTCCC
*
25944 ATTATATGGCTCTTCGTGAGCTTACCG
1 ATTA-ATGGCTCTTCGTGAGCTTACCA
* * *
25971 ATTAAAGACTCTTTGTGAGCTT-CCAA
1 ATTAATGGCTCTTCGTGAGCTTACC-A
25997 ATTAATGGCTCTTC
1 ATTAATGGCTCTTC
26011 AGAGTTTCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 2 0.06
26 26 0.81
27 4 0.12
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (26 bp):
ATTAATGGCTCTTCGTGAGCTTACCA
Found at i:29071 original size:50 final size:50
Alignment explanation
Indices: 28949--29073 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
28939 TTATTGAGGT
* * * * *
28949 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 TATGAGAGGTCCCACGTAAGACTATGTCTAGAACATGGCATGGGCACCGA
* * *
28999 GATGAGAGGTCCCCCGTAAGACTATGTCTAGAACATGGCATGGGCACTGA
1 TATGAGAGGTCCCACGTAAGACTATGTCTAGAACATGGCATGGGCACCGA
** *
29049 TATGAGAACTCCCATGTAAGACTAT
1 TATGAGAGGTCCCACGTAAGACTAT
29074 CTGGGATATG
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACTATGTCTAGAACATGGCATGGGCACCGA
Done.