Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2091
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: 67473
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:21928 original size:40 final size:39
Alignment explanation
Indices: 21845--22026 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 39
21835 TTGAATGCTG
* * * *
21845 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
21883 ATCCGGACTAAGATCCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
21924 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTATTAAT
* *
21964 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTATT-AAT
22003 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGT-CCGAAGGCATT
22027 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.01
39 43 0.36
40 68 0.56
41 9 0.07
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (39 bp):
TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:21979 original size:79 final size:81
Alignment explanation
Indices: 21845--22023 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
21835 TTGAATGCTG
* * *
21845 TCCGGGCTAAGT-CCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
21908 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
21924 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGATCCGAAGGCA
21985 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTTTAAAA
22003 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
22024 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
78 2 0.02
79 55 0.62
80 22 0.25
81 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:22059 original size:79 final size:79
Alignment explanation
Indices: 21885--22063 Score: 193
Period size: 79 Copynumber: 2.3 Consensus size: 79
21875 GTGACTATAT
* * * * *
21885 CCGGACTAAGATCCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTG
1 CCGGGCTAAG-TCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTG
** *
21950 TGCGAGATACTAATT
65 AACGAGATACTAATA
*
21965 CCGGGTTAAGTCCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGG-CATTG
1 CCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCCATTG
* *
22028 AATGAGTTACT-ATGA
65 AACGAGATACTAAT-A
*
22043 CCGGGCTATGTCCCGAAGGCA
1 CCGGGCTAAGT-CCGAAGGCA
22064 CTTGAACGAG
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
77 2 0.02
78 22 0.27
79 51 0.61
80 8 0.10
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGA
ACGAGATACTAATA
Found at i:27019 original size:28 final size:28
Alignment explanation
Indices: 26956--27078 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
26946 ATATTAAGTC
*
26956 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
26983 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
27011 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
27039 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
27068 CGCACACTTAG
1 CGCACACTTAG
27079 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31440 original size:41 final size:42
Alignment explanation
Indices: 31393--31471 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 42
31383 CTCGATATAT
*
31393 TATATATCCGGGTTAAATCCCGC-GGCTTCGTGCTGGTCATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTCATA
*
31434 TATATATCCGGGTTAAATCCTGCAGGCTTAGTGCTGGT
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGT
31472 ACTATATCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 22 0.63
42 13 0.37
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (42 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTCATA
Found at i:42933 original size:79 final size:81
Alignment explanation
Indices: 42804--43010 Score: 246
Period size: 79 Copynumber: 2.6 Consensus size: 81
42794 GGAATTTAAA
* * *
42804 CGGATATAGCT-ACTT-GCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAAT
1 CGGATATAG-TAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAAT
42867 GCCTTCGGGA-CTTAACC
65 GCCTTC-GGATCTTAACC
* * *
42884 CGGATTTAGTAAC-TCGCACCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAAT
1 CGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAAT
**
42946 GCCTTCGGATCTTAGTC
65 GCCTTCGGATCTTAACC
* * *
42963 CGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCAGATAT
1 CGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
43011 CATTCGAATA
Statistics
Matches: 107, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
78 4 0.04
79 50 0.47
80 41 0.38
81 11 0.10
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (81 bp):
CGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
CCTTCGGATCTTAACC
Found at i:42936 original size:39 final size:40
Alignment explanation
Indices: 42804--43010 Score: 242
Period size: 40 Copynumber: 5.2 Consensus size: 40
42794 GGAATTTAAA
* * *
42804 CGGATATAGCT-ACTTGCTCAAATGCCTTCGGGACATAGCC
1 CGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
42844 CGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
42884 CGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
*
42923 CGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTC
1 CGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCC
* * *
42963 CGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCC
1 CGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
*
43004 CAGATAT
1 CGGATAT
43011 CATTCGAATA
Statistics
Matches: 143, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 78 0.55
41 27 0.19
42 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
Found at i:43842 original size:23 final size:22
Alignment explanation
Indices: 43815--43859 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
43805 AATATATAGG
*
43815 TCATACCAATACATCATGTGCAA
1 TCATACAAATACAT-ATGTGCAA
* *
43838 TCATATAAATATATATGTGCAA
1 TCATACAAATACATATGTGCAA
43860 GAGCCGAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (22 bp):
TCATACAAATACATATGTGCAA
Found at i:45981 original size:16 final size:16
Alignment explanation
Indices: 45925--45981 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
45915 CACGACTCGT
*
45925 TTTATTTATTATTT-TC
1 TTTATTT-TTATTTCTA
* *
45941 TTTACTTTTATATCTA
1 TTTATTTTTATTTCTA
45957 TTTATTTTTATTTCTA
1 TTTATTTTTATTTCTA
45973 TTTATTTTT
1 TTTATTTTT
45982 GAAGACTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 5 0.14
16 30 0.86
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTTATTTCTA
Found at i:48360 original size:49 final size:48
Alignment explanation
Indices: 48230--48373 Score: 171
Period size: 49 Copynumber: 2.9 Consensus size: 48
48220 TCCAATGTGA
*
48230 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC---AGACTGT
* * * * * *
48281 GATCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGACTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTG-T
* *
48330 GGTCGCATGTGTAGTGCTAAGTGTAGGCTACTATGCGTACCAGA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
48374 TAGCTTCGGC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
48 5 0.06
49 37 0.48
51 35 0.45
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTGT
Found at i:63096 original size:31 final size:31
Alignment explanation
Indices: 63061--63122 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
63051 ATTTAATACG
63061 AACTTTAAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAAATTACACTTTTGCCCCTA
**** *
63092 AACTTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAAATTACACTTTTGCCCCTA
63123 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (31 bp):
AACTTTAAAAAAAATTACACTTTTGCCCCTA
Done.