Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2887
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: 39581
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:3981 original size:20 final size:20
Alignment explanation
Indices: 3958--4004 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3948 GGGTTAAGAT
*
3958 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
3978 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
3998 TGAGCTG
1 TGAGCTG
4005 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:5701 original size:48 final size:48
Alignment explanation
Indices: 5649--5754 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
5639 TTGTCTTTTC
*
5649 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
5697 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
5745 TTTCTTTTTC
1 TTTCTTTTTC
5755 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:6792 original size:12 final size:12
Alignment explanation
Indices: 6772--6889 Score: 67
Period size: 12 Copynumber: 9.2 Consensus size: 12
6762 CTCGCAAGAC
6772 TTTTCACTTTTT
1 TTTTCACTTTTT
*
6784 TTTTAACTTGATTTT
1 TTTTCAC-T--TTTT
* *
6799 TTTTCTCATTTT
1 TTTTCACTTTTT
**
6811 TTTTCTTTTTTT
1 TTTTCACTTTTT
6823 TTTTCACTTTTT
1 TTTTCACTTTTT
* *
6835 TTTTGAATTTTT
1 TTTTCACTTTTT
*
6847 TTTCAATCAATTTTTT
1 TTT---TC-ACTTTTT
*
6863 TTTTCGAATTTTT
1 TTTTC-ACTTTTT
*
6876 TTTTGA-TTTTT
1 TTTTCACTTTTT
6887 TTT
1 TTT
6890 GTTACTCCAA
Statistics
Matches: 84, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
11 8 0.10
12 44 0.52
13 13 0.15
15 10 0.12
16 9 0.11
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTCACTTTTT
Found at i:6847 original size:14 final size:14
Alignment explanation
Indices: 6830--6879 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
6820 TTTTTTTCAC
6830 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
** *
6844 TTTTTTCAATCAATT
1 TTTTTT-TTTGAATT
*
6859 TTTTTTTTCGAATT
1 TTTTTTTTTGAATT
6873 TTTTTTT
1 TTTTTTT
6880 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:10197 original size:27 final size:28
Alignment explanation
Indices: 10127--10197 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
10117 AATAGTGAGA
*
10127 GAAAAAGAAAATGA-AGAAAAGAAAATT
1 GAAAAAGAAAAAGATAGAAAAGAAAATT
*
10154 GAAAAAGAAATTGAGATTAG-AAA-AAAATT
1 GAAAAAGAAA--AAGA-TAGAAAAGAAAATT
10183 GAAAAAGAAAAAGAT
1 GAAAAAGAAAAAGAT
10198 GTTGAAGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.03
27 13 0.35
29 18 0.49
30 3 0.08
31 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (28 bp):
GAAAAAGAAAAAGATAGAAAAGAAAATT
Found at i:16291 original size:11 final size:11
Alignment explanation
Indices: 16275--16300 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16265 CTGCGTCACA
16275 GTTTAATAATT
1 GTTTAATAATT
16286 GTTTAATAATT
1 GTTTAATAATT
16297 GTTT
1 GTTT
16301 TCTAGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (11 bp):
GTTTAATAATT
Found at i:24336 original size:11 final size:11
Alignment explanation
Indices: 24320--24356 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
24310 ATACTTCAAA
24320 TTTTGAATTTT
1 TTTTGAATTTT
24331 TTTTGAATTTT
1 TTTTGAATTTT
24342 TTTTGAATTTT
1 TTTTGAATTTT
24353 TTTT
1 TTTT
24357 TCAAATTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:26236 original size:10 final size:10
Alignment explanation
Indices: 26221--26279 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
26211 TACTAAATAC
26221 CATACCATTT
1 CATACCATTT
*
26231 CATACCAATTC
1 CATACC-ATTT
26242 CATACCATTT
1 CATACCATTT
* *
26252 CGTACCAATTC
1 CATACC-ATTT
26263 CATACCATTT
1 CATACCATTT
*
26273 CGTACCA
1 CATACCA
26280 ATTCCCAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 23 0.57
11 17 0.43
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.32
Consensus pattern (10 bp):
CATACCATTT
Found at i:26245 original size:21 final size:21
Alignment explanation
Indices: 26201--26351 Score: 169
Period size: 21 Copynumber: 7.0 Consensus size: 21
26191 TTTGAACCAT
* * *
26201 TACCAATTCGTACTAAATACCA
1 TACCATTTCGTAC-CAATTCCA
*
26223 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
26244 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
26265 TACCATTTCGTACCAATTCCCAAA
1 TACCATTTCGTACCAATT-CC--A
** *
26289 TACCGA-AACGTACCAAATACCA
1 TACC-ATTTCGTACC-AATTCCA
*
26311 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
26332 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
26352 CAAATACCAA
Statistics
Matches: 110, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
21 70 0.64
22 23 0.21
24 13 0.12
25 4 0.04
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:26319 original size:67 final size:67
Alignment explanation
Indices: 26233--26387 Score: 251
Period size: 67 Copynumber: 2.3 Consensus size: 67
26223 TACCATTTCA
* * *
26233 TACC-AATTCCATACCATTTCGTACCAATTCCATACCATTTCGTACCAATTCCCAAATACCGAAA
1 TACCAAATACCATACCATTTCATACCAATTCCATACCATTTCGTACCAATTCCCAAATACCAAAA
26297 CG
66 CG
26299 TACCAAATACCATACCATTTCATACCAATTCCATACCATTTCGTACCAATTCCCAAATACCAAAA
1 TACCAAATACCATACCATTTCATACCAATTCCATACCATTTCGTACCAATTCCCAAATACCAAAA
26364 CG
66 CG
26366 TACCAAA-ACCAAATACCATTTC
1 TACCAAATACC--ATACCATTTC
26388 TTAATTATCC
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
66 7 0.08
67 66 0.80
68 10 0.12
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (67 bp):
TACCAAATACCATACCATTTCATACCAATTCCATACCATTTCGTACCAATTCCCAAATACCAAAA
CG
Found at i:27501 original size:15 final size:15
Alignment explanation
Indices: 27469--27502 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27459 GTTCAACGAA
*
27469 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
27484 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
27499 GAGG
1 GAGG
27503 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:31199 original size:10 final size:10
Alignment explanation
Indices: 31184--31245 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
31174 TTTGAACCAT
*
31184 TACCAATTCG
1 TACCAATTCA
*
31194 TACCAAATACCA
1 TACC-AAT-TCA
*
31206 TACCATTTCA
1 TACCAATTCA
31216 TACCAATTCCA
1 TACCAATT-CA
* *
31227 TACCATTTCG
1 TACCAATTCA
31237 TACCAATTC
1 TACCAATTC
31246 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:31229 original size:21 final size:21
Alignment explanation
Indices: 31184--31246 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31174 TTTGAACCAT
* *
31184 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
31206 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
31227 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
31247 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:34091 original size:4 final size:4
Alignment explanation
Indices: 34082--34109 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
34072 AAGTTTTATT
34082 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
34110 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Done.