Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold495
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: 36773
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2397 original size:42 final size:39
Alignment explanation
Indices: 2337--2442 Score: 133
Period size: 39 Copynumber: 2.6 Consensus size: 39
2327 CTCGAATGAT
* *
2337 ATCCGGGCTAAGTCCGAAGGCTTTTGCGCTAAGCGACTAC
1 ATCCGGGCTAAGTCCGAAGGCATTTGCGCT-AGCAACTAC
* *
2377 ATCCGGGACTAAGATCCGAAGGCATTTGTGCTAGCAACTAT
1 ATCCGGG-CTAAG-TCCGAAGGCATTTGCGCTAGCAACTAC
2418 AT-CGGGCTAAGTCCCGAAGGCATTT
1 ATCCGGGCTAAGT-CCGAAGGCATTT
2443 CATGCTAGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 17 0.29
40 11 0.19
41 14 0.24
42 16 0.27
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (39 bp):
ATCCGGGCTAAGTCCGAAGGCATTTGCGCTAGCAACTAC
Found at i:2460 original size:40 final size:40
Alignment explanation
Indices: 2335--2479 Score: 123
Period size: 41 Copynumber: 3.6 Consensus size: 40
2325 TACTCGAATG
* * ** * *
2335 ATATCCGGGCTAAG-TCCGAAGGCTTTTGCGCTAAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCT-AGCAACC
* * * *
2375 ACATCCGGGACTAAGATCCGAAGGCATTTGTGCTAGCAACT
1 ATATCCGGG-CTAAGACCCGAAGGCATTTATGCTAGCAACC
* **
2416 ATAT-CGGGCTAAGTCCCGAAGGCATTTCATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTT-ATGCTAGCAACC
*
2456 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
2480 CTTGTGGCGA
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
39 17 0.19
40 24 0.27
41 31 0.35
42 16 0.18
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCAACC
Found at i:10356 original size:40 final size:40
Alignment explanation
Indices: 10262--10406 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
10252 TACTCGAATG
*
10262 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
10303 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
** * *
10343 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
10383 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
10407 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.67
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:12227 original size:40 final size:40
Alignment explanation
Indices: 12172--12345 Score: 267
Period size: 40 Copynumber: 4.3 Consensus size: 40
12162 ATGTGCACAT
* * *
12172 CATTCGTGCGGGTTATTATAACCAGGTTAAGTCTCGAAGG
1 CATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAGG
12212 CATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAGG
1 CATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAGG
*
12252 CATTCGTGCGGGTTATTATAATCGGGCTAAGTCCCGAAGG
1 CATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAGG
* * * *
12292 CATTCATGCGAGTTATTATTACCGGGTTAAGTCCCGAAGG
1 CATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAGG
*
12332 CATTCGTGCTGGTT
1 CATTCGTGCGGGTT
12346 GTTACATCCG
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
CATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAGG
Found at i:12369 original size:80 final size:80
Alignment explanation
Indices: 12172--12369 Score: 220
Period size: 80 Copynumber: 2.5 Consensus size: 80
12162 ATGTGCACAT
* ** * * * *
12172 CATTCGTGCGGGTTATTATAA-CCAGGTTAAGTCTCGAAGGCATTCGTGCGGGTTATTATAACCG
1 CATTCGTGCGGGTTATTATAATCGA-GCCAAATCCCGAAGGCATTCATGCGAGTTATTATAACCG
12236 GGCTAAGTCCCGAAGG
65 GGCTAAGTCCCGAAGG
* * * *
12252 CATTCGTGCGGGTTATTATAATCGGGCTAAGTCCCGAAGGCATTCATGCGAGTTATTATTACCGG
1 CATTCGTGCGGGTTATTATAATCGAGCCAAATCCCGAAGGCATTCATGCGAGTTATTATAACCGG
*
12317 GTTAAGTCCCGAAGG
66 GCTAAGTCCCGAAGG
* * * *
12332 CATTCGTGCTGGTTGTTA-CATCCGAGCCAAATTCCGAA
1 CATTCGTGCGGGTTATTATAAT-CGAGCCAAATCCCGAA
12370 AGTATTTATG
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
79 2 0.02
80 98 0.97
81 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
CATTCGTGCGGGTTATTATAATCGAGCCAAATCCCGAAGGCATTCATGCGAGTTATTATAACCGG
GCTAAGTCCCGAAGG
Found at i:27485 original size:47 final size:47
Alignment explanation
Indices: 27371--27540 Score: 169
Period size: 45 Copynumber: 3.7 Consensus size: 47
27361 GCCCCTAAGT
* * * *
27371 GAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCC--AAGC
27417 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTC-A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATC-CAAGC
* *
27464 GAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCATAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA-AGC
27509 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC
27541 TCAACCATCC
Statistics
Matches: 105, Mismatches: 6, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 2 0.02
45 29 0.28
46 27 0.26
47 29 0.28
48 2 0.02
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCAAGC
Found at i:27540 original size:92 final size:93
Alignment explanation
Indices: 27371--27540 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
27361 GCCCCTAAGT
* *
27371 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27436 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
27464 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27528 CGAGTTCGGATGC
66 CGAGTTCGGATGC
27541 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 35 0.47
93 39 0.53
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:35002 original size:93 final size:93
Alignment explanation
Indices: 34895--35065 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
34885 GCCCCTAAGT
* *
34895 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
34960 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
34988 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
35053 CGAGTTCGGATGC
66 CGAGTTCGGATGC
35066 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:35062 original size:46 final size:46
Alignment explanation
Indices: 34890--35062 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
34880 AACCCGCCCC
* * *
34890 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
34936 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
34984 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
35029 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
35063 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:35515 original size:31 final size:30
Alignment explanation
Indices: 35480--35540 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35470 ATTTAATACG
35480 AACTTTGGAAAAAATTACACTTTTGCCCCTA
1 AACTTTGG-AAAAATTACACTTTTGCCCCTA
* * *
35511 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
35541 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.