Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2004
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: 38500
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Found at i:294 original size:40 final size:40
Alignment explanation
Indices: 189--397 Score: 289
Period size: 39 Copynumber: 5.5 Consensus size: 40
179 AAACCAAGTA
*
189 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCG--CAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
226 CCTTC-GGACTTAGCCC-GATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
264 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
304 CCTTCGGGACTTAGCCC-GATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
343 CCTTCGGG-CTTAG-CCGGA-ATTAGTCACTAGCACAAAT-
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
380 CCTT-GGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
398 TTATCATCCG
Statistics
Matches: 159, Mismatches: 3, Indels: 19
0.88 0.02 0.10
Matches are distributed among these distances:
35 1 0.01
36 22 0.14
37 19 0.12
38 37 0.23
39 41 0.26
40 39 0.25
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:326 original size:79 final size:77
Alignment explanation
Indices: 189--396 Score: 304
Period size: 79 Copynumber: 2.7 Consensus size: 77
179 AAACCAAGTA
*
189 CCTTCGGGATTTAGCCGGATATAGCTACTCG--CAAATGCCTTC-GGACTTAGCCCGATATAGTA
1 CCTTCGGGACTTAGCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGTA
251 ACTCGCACAAATG
65 ACTCGCACAAATG
264 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGT
1 CCTTCGGGACTTAG-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGT
329 AACTCGCACAAATG
64 AACTCGCACAAATG
*
343 CCTTCGGG-CTTAGCCGGA-ATTAGTCACTAGCACAAAT-CCTT-GGGACTTAGCCCG
1 CCTTCGGGACTTAGCCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCG
397 GTTATCATCC
Statistics
Matches: 124, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
75 27 0.22
76 20 0.16
77 20 0.16
78 16 0.13
79 41 0.33
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (77 bp):
CCTTCGGGACTTAGCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGTAA
CTCGCACAAATG
Found at i:8223 original size:40 final size:40
Alignment explanation
Indices: 8153--8370 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
8143 AAACCAAGTA
* *
8153 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
8192 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
8232 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
8272 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
8312 CCTTCGGGGCTTAGCTCGGA-ATTAGTCACTAGCCCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
8352 CCTTTGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
8371 TTATCATCCG
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 145 0.91
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:24207 original size:22 final size:21
Alignment explanation
Indices: 24169--24209 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
24159 CTCTTAACAC
* *
24169 AGGGGCACACGCCCGTGTGGG
1 AGGGGCACACACACGTGTGGG
24190 AGGGGCAACACACACGTGTG
1 AGGGGC-ACACACACGTGTG
24210 ACATTTCAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.22, C:0.27, G:0.41, T:0.10
Consensus pattern (21 bp):
AGGGGCACACACACGTGTGGG
Found at i:27696 original size:27 final size:27
Alignment explanation
Indices: 27655--27838 Score: 199
Period size: 27 Copynumber: 6.8 Consensus size: 27
27645 AAACATACAT
*
27655 CACATAGGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
27682 CATATAAGGGCAAAATAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * *
27709 CACATAAGGGTAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
*
27736 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
*
27763 CCCATAAGGGCAAAACAGTCAT-TGTAC
1 CACATAAGGGCAAAACAGTCATCT-TAC
* * * * * * *
27790 CCCATAAGGGTAACATAATCATTTTTC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
27817 CTCATAAGGGCAAAATAGTCAT
1 CACATAAGGGCAAAACAGTCAT
27839 ATTATTGATT
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 135 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATCTTAC
Found at i:27753 original size:81 final size:81
Alignment explanation
Indices: 27655--27838 Score: 253
Period size: 81 Copynumber: 2.3 Consensus size: 81
27645 AAACATACAT
* * *
27655 CACATAGGGGCAAAACAGTCATCTTACCATATAAGGGCAAAATAGTCATCT-TACCACATAAGGG
1 CACATAAGGGCAAAACAGTCATCTTACCACATAAGGGCAAAACAGTCAT-TGTACCACATAAGGG
*
27719 TAAAATAGTCATTTTAC
65 TAAAATAATCATTTTAC
* * *
27736 CACATAAGGGCAAAACAGTCATTTTACCCCATAAGGGCAAAACAGTCATTGTACCCCATAAGGGT
1 CACATAAGGGCAAAACAGTCATCTTACCACATAAGGGCAAAACAGTCATTGTACCACATAAGGGT
* *
27801 AACATAATCATTTTTC
66 AAAATAATCATTTTAC
* *
27817 CTCATAAGGGCAAAATAGTCAT
1 CACATAAGGGCAAAACAGTCAT
27839 ATTATTGATT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 90 0.99
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (81 bp):
CACATAAGGGCAAAACAGTCATCTTACCACATAAGGGCAAAACAGTCATTGTACCACATAAGGGT
AAAATAATCATTTTAC
Found at i:30648 original size:103 final size:103
Alignment explanation
Indices: 30395--30759 Score: 614
Period size: 103 Copynumber: 3.6 Consensus size: 103
30385 TAGCCGTTAT
*
30395 TGGTGGAT-CCGCACTTAGCACCACC-ATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
30458 AATCAGCACATAGCAACCCCCTTTT-ATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
30495 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
30560 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
30598 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
30662 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
30701 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
30760 TTTATATACA
Statistics
Matches: 253, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
100 8 0.03
101 16 0.06
102 91 0.36
103 137 0.54
104 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:30660 original size:26 final size:26
Alignment explanation
Indices: 30630--30681 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
30620 CACCAATGAA
*
30630 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
30656 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
30682 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:31120 original size:29 final size:29
Alignment explanation
Indices: 31087--31150 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
31077 TAATCCACCA
31087 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
31116 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
31146 CCCAA
1 CCCAA
31151 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:31124 original size:30 final size:30
Alignment explanation
Indices: 31094--31150 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31084 CCACCCAACT
31094 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
31123 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
31151 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:38133 original size:93 final size:95
Alignment explanation
Indices: 37974--38248 Score: 402
Period size: 93 Copynumber: 2.9 Consensus size: 95
37964 ATTGGTGATC
37974 CGCACTTAGCACCACC-ACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
1 CGCACTTAGCACCACCAACTGAATC-GGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
38038 ATAGCAACCCCCTTTCAAAGATA-T-GATAT
65 ATAGCAACCCCCTTTCAAAGATAGTGGATAT
38067 CGCACTTAGCACCACCATACTGCAATC-GGAATCAGCACTTAGCAACCCCTC-GGGGAATCAGCA
1 CGCACTTAGCACCACCA-ACTG-AATCGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCA
38130 CATAGCAACCCCCTTTCATTTCAAAGATATGGTGGATAT
64 CATAGCAA-CCCC---C-TTTCAAAGATA--GTGGATAT
38169 CGCACTTAGCACCACCAA-TGAA-CGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
1 CGCACTTAGCACCACCAACTGAATC-GGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
38232 ATAGCAACCCCCTTTCA
65 ATAGCAACCCCCTTTCA
38249 CATTTCAAAG
Statistics
Matches: 167, Mismatches: 0, Indels: 27
0.86 0.00 0.14
Matches are distributed among these distances:
93 36 0.22
94 28 0.17
95 4 0.02
96 9 0.05
97 2 0.01
98 12 0.07
99 2 0.01
100 30 0.18
101 22 0.13
102 22 0.13
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (95 bp):
CGCACTTAGCACCACCAACTGAATCGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
TAGCAACCCCCTTTCAAAGATAGTGGATAT
Found at i:38282 original size:103 final size:100
Alignment explanation
Indices: 37966--38319 Score: 464
Period size: 103 Copynumber: 3.6 Consensus size: 100
37956 TTACCGTTAT
*
37966 TGGTGATCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
1 TGGTGAT-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
38031 TCAGCACATAGCAA--CCC---CC-TTTCAAAGATA
65 TCAGCACATAGCAACCCCCTTTCCATTTCAAAGATA
*
38061 TGAT-ATCGCACTTAGCACCACCATACTGCAATC--GGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGATCGCACTTAGCACCACCA-A-TG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
38122 AATCAGCACATAGCAACCCCCTTT-CATTTCAAAGATA
63 AATCAGCACATAGCAACCCCCTTTCCATTTCAAAGATA
38159 TGGTGGATATCGCACTTAGCACCACCAATGAA-CGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGT-G--ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
38223 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
63 AATCAGCACATAGCAACCCCCTTTC-CATTTCAAAGATA
* * **
38262 TGGTGGATCACGCACATAGCACCACC-ATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGT-GAT--CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
38320 TTTATATACA
Statistics
Matches: 231, Mismatches: 7, Indels: 34
0.85 0.03 0.12
Matches are distributed among these distances:
93 37 0.16
94 26 0.11
95 8 0.03
96 4 0.02
97 1 0.00
98 15 0.06
99 2 0.01
100 26 0.11
101 31 0.13
102 23 0.10
103 58 0.25
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (100 bp):
TGGTGATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT
CAGCACATAGCAACCCCCTTTCCATTTCAAAGATA
Found at i:38481 original size:20 final size:21
Alignment explanation
Indices: 38436--38482 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
38426 ACATTTATTT
* * *
38436 TAATTCAAATAAATCTCAACA
1 TAATACAAATAAATATCAAAA
38457 T-ATACAAAT-AATATCAAAA
1 TAATACAAATAAATATCAAAA
38476 TAATACA
1 TAATACA
38483 TTAAGTCACG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.41
20 12 0.55
21 1 0.05
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
TAATACAAATAAATATCAAAA
Done.