Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold678
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: 47977
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Found at i:6042 original size:39 final size:39
Alignment explanation
Indices: 5941--6117 Score: 180
Period size: 39 Copynumber: 4.5 Consensus size: 39
5931 ATATCCGGAC
* *
5941 TAAGATCCGAAGGCATTTGTGCGAGATA-CAAGTTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATATTAA-ATCCGGGT
* *
5981 TAAGCCCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATATTAAATCCGGGT
*
6021 TAAGTCCGAAGGCATTCGTGCGAG-TCATTAAATCCGGGT
1 TAAGTCCGAAGGCATTTGTGCGAGAT-ATTAAATCCGGGT
* * * * *
6060 TAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATATTAAATCCGGGT
*
6099 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
6118 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.01
39 66 0.56
40 49 0.42
41 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATATTAAATCCGGGT
Found at i:6057 original size:79 final size:77
Alignment explanation
Indices: 5935--6115 Score: 195
Period size: 79 Copynumber: 2.3 Consensus size: 77
5925 GTGAATATAT
* * *
5935 CCGGACTAAGATCCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTG
1 CCGGGCTAAG-TCCGAAGGCATTCGTGCGAGATACAAG-TCCGGGTTAAGCCCCGAAGG-CATTG
* *
6000 TGCGAGATATTAAAT
63 TGCGAGATACTAAAA
* *
6015 CCGGGTTAAGTCCGAAGGCATTCGTGCGAGTCATTA-AA-TCCGGGTTAAGTCCCGAAGGCATTG
1 CCGGGCTAAGTCCGAAGGCATTCGTGCGAG--A-TACAAGTCCGGGTTAAGCCCCGAAGGCATTG
* *
6078 TGTGAGTTACTAAAA
63 TGCGAGATACTAAAA
*
6093 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGT-CCGAAGGCATT
6116 TGAACGAGGA
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 24 0.28
79 49 0.57
80 8 0.09
81 3 0.03
82 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (77 bp):
CCGGGCTAAGTCCGAAGGCATTCGTGCGAGATACAAGTCCGGGTTAAGCCCCGAAGGCATTGTGC
GAGATACTAAAA
Found at i:16329 original size:40 final size:40
Alignment explanation
Indices: 16246--16461 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
16236 CAACCAAGTA
** *
16246 CCTTCGGGGTTTAG-CCGGATATAGCT-ACT-GCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
16284 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
16324 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
16364 CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
16404 CCTTTGGG-CTTAGCCTGGA-ATTAGTCACTTGCACAGATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
16443 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
16462 TTATCATCCG
Statistics
Matches: 157, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
38 14 0.09
39 42 0.27
40 101 0.64
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:23101 original size:40 final size:40
Alignment explanation
Indices: 23018--23232 Score: 262
Period size: 40 Copynumber: 5.5 Consensus size: 40
23008 CAACCAAGTA
** *
23018 CCTTCGGGGTTTAG-CCGGATATAGCT-ACT-GCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
23056 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
23096 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
23136 CCTTCGGGACTTAGCCCGGATATAATAACTCACACAATTT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
23176 CCTTCGGG-CTTAGCCC-GAAATTAGTCACTTGCA-AGATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
23214 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
23233 TTATCATCCG
Statistics
Matches: 154, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
38 26 0.17
39 36 0.23
40 92 0.60
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27783 original size:55 final size:56
Alignment explanation
Indices: 27718--27832 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
27708 AGCATGGCTG
* *
27718 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
27774 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
27829 CCAG
1 CCAG
27833 GATGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:27795 original size:27 final size:27
Alignment explanation
Indices: 27743--27832 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
27733 GTGACAGAGT
27743 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
27772 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
27799 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
27827 CACCAG
1 CACCAG
27833 GATGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:27985 original size:28 final size:28
Alignment explanation
Indices: 27938--28030 Score: 152
Period size: 28 Copynumber: 3.3 Consensus size: 28
27928 AAATTAACCC
*
27938 TAGGGGTATAGA-GGTCATTTTGCATACA
1 TAGGGGTATA-ATGGTAATTTTGCATACA
27966 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
27994 TAGGGGTCTAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
28022 TAGGGGTAT
1 TAGGGGTAT
28031 TCTAGTACAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 1 0.02
28 60 0.98
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:36454 original size:13 final size:13
Alignment explanation
Indices: 36436--36467 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
36426 ACAAATTGAT
36436 GTCACACGGCCAA
1 GTCACACGGCCAA
36449 GTCACACGGCCAA
1 GTCACACGGCCAA
36462 GTCACA
1 GTCACA
36468 TGCCCATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.22, T:0.09
Consensus pattern (13 bp):
GTCACACGGCCAA
Done.