Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3657
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: 28754
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:5063 original size:29 final size:29
Alignment explanation
Indices: 4969--5123 Score: 113
Period size: 29 Copynumber: 5.4 Consensus size: 29
4959 TCTCATTTCA
* * *
4969 CACACTTAGTGCC-CACTAACCGATCTCG
1 CACACATAGTGCCTCAATTACCGATCTCG
** * *
4997 CACACATAGTG-CTCGGTTGA-AGAACTCG
1 CACACATAGTGCCTCAATT-ACCGATCTCG
5025 CACACATAGTGCCTCAATTACCGATCTCG
1 CACACATAGTGCCTCAATTACCGATCTCG
* * ** *
5054 CACACATAGTG-ATCAGTTAAAGGAAT-TTG
1 CACACATAGTGCCTCAATT-ACCG-ATCTCG
* * *
5083 CACACACAGTGCCTCAATTATCGATCTCA
1 CACACATAGTGCCTCAATTACCGATCTCG
5112 CACACATAGTGC
1 CACACATAGTGC
5124 TCGGTTAAAA
Statistics
Matches: 96, Mismatches: 23, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
27 1 0.01
28 37 0.39
29 51 0.53
30 7 0.07
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (29 bp):
CACACATAGTGCCTCAATTACCGATCTCG
Found at i:5108 original size:58 final size:57
Alignment explanation
Indices: 4987--5155 Score: 239
Period size: 58 Copynumber: 2.9 Consensus size: 57
4977 GTGCCCACTA
* * * *
4987 ACCGATCTCGCACACATAGTGCTCGGTTGAAGAACTCGCACACATAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTTGCACACACAGTGCCTCAATT
* *
5044 ACCGATCTCGCACACATAGTGATCAGTTAAAGGAATTTGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAA-GAATTTGCACACACAGTGCCTCAATT
* * *
5102 ATCGATCTCACACACATAGTGCTCGGTTAAAATAATTTGCACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTT-AAAGAATTTGCACACACAGTGCCTC
5156 TAATCATTCG
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
57 28 0.28
58 68 0.69
59 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (57 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTTGCACACACAGTGCCTCAATT
Found at i:5370 original size:43 final size:43
Alignment explanation
Indices: 5309--5485 Score: 300
Period size: 43 Copynumber: 4.1 Consensus size: 43
5299 CCTTGCTCGA
** *
5309 ATCACCGGCATTAAGCCTGCTAGGCACGAAGACCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
5352 ATCACCGGCACGAAGCCTGCTAGGCATGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
5395 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
5438 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGTCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
5481 ATCAC
1 ATCAC
5486 TAAGTTTCAT
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 126 1.00
ACGTcount: A:0.32, C:0.33, G:0.23, T:0.12
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:13215 original size:27 final size:27
Alignment explanation
Indices: 13180--13248 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
13170 AAGTGTACTG
* *
13180 TACTAGTGGCTTTGCCACATATACTAT
1 TACTGGTGGCTTTGCCACATACACTAT
*
13207 TACTGGTGGCTTTGCCACATACACTGT
1 TACTGGTGGCTTTGCCACATACACTAT
*
13234 TACTGGTAGCTTTGC
1 TACTGGTGGCTTTGC
13249 TGCGTTACTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (27 bp):
TACTGGTGGCTTTGCCACATACACTAT
Found at i:13515 original size:32 final size:33
Alignment explanation
Indices: 13453--13518 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
13443 TTACTGTTTC
13453 GTAATGGGCTCAAGCCCAAACTATTACTGATCT
1 GTAATGGGCTCAAGCCCAAACTATTACTGATCT
* * *
13486 GTAATGGGCTCAGGCCC-GATTATTACTGATCT
1 GTAATGGGCTCAAGCCCAAACTATTACTGATCT
13518 G
1 G
13519 GGCTAAGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (33 bp):
GTAATGGGCTCAAGCCCAAACTATTACTGATCT
Found at i:14077 original size:7 final size:7
Alignment explanation
Indices: 14067--14091 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
14057 TTGGGGTGCT
14067 ACATATC
1 ACATATC
14074 ACATATC
1 ACATATC
14081 ACATATC
1 ACATATC
14088 ACAT
1 ACAT
14092 GTTGCGCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATATC
Found at i:24204 original size:40 final size:40
Alignment explanation
Indices: 24081--24344 Score: 293
Period size: 40 Copynumber: 6.6 Consensus size: 40
24071 TGAATGCTGC
* * * * *
24081 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAAT
** * * *
24121 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGTT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAA-AT
* *
24161 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
*
24201 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
* *
24241 CCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTATTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
* * *
24281 CCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
* *
24320 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGTTAAGTCCCGAAGGCATTTG
24345 AACGAGGAGC
Statistics
Matches: 195, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 35 0.18
40 150 0.77
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
Found at i:24362 original size:79 final size:80
Alignment explanation
Indices: 24081--24377 Score: 228
Period size: 80 Copynumber: 3.7 Consensus size: 80
24071 TGAATGCTGC
* ** * * **
24081 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * **
24144 TGTGCGAGATAC-AAGTT
64 CGTGCGAGTTACTAA-AA
* * * * ** * *
24161 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
* *
24226 TGCGAGTTATTAAAT
66 TGCGAGTTACTAAAA
* *** * *
24241 CCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
24305 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
24320 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
24378 TACGTGATTT
Statistics
Matches: 184, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
78 16 0.09
79 45 0.24
80 114 0.62
81 9 0.05
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Done.