Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2566
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: 33305
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:3826 original size:39 final size:41
Alignment explanation
Indices: 3725--3908 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
3715 TTGAATGATG
* *
3725 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
3765 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
3805 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
3844 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
3883 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3909 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:3861 original size:79 final size:80
Alignment explanation
Indices: 3725--3908 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
3715 TTGAATGATG
*
3725 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
3789 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
3804 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
3866 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
3883 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3909 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:3931 original size:78 final size:79
Alignment explanation
Indices: 3778--3941 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
3768 GGACTAAGAT
* **
3778 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
3843 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
3857 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
3919 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
3935 CCGAAGG
1 CCGAAGG
3942 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:11777 original size:79 final size:81
Alignment explanation
Indices: 11641--11825 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
11631 TTGAATGATG
* *
11641 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
11705 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
11720 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
11782 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
11800 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11826 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:11839 original size:40 final size:40
Alignment explanation
Indices: 11642--11825 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
11632 TGAATGATGT
* * * *
11642 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
11682 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
11722 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
11760 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
11801 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
11826 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:11847 original size:79 final size:79
Alignment explanation
Indices: 11694--11858 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
11684 GGACTAAGAT
* * **
11694 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
11759 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
11773 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
11836 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
11852 CCGAAGG
1 CCGAAGG
11859 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:15717 original size:11 final size:11
Alignment explanation
Indices: 15701--15725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15691 TTAATTTAAT
15701 ATTATTTAAAA
1 ATTATTTAAAA
15712 ATTATTTAAAA
1 ATTATTTAAAA
15723 ATT
1 ATT
15726 TTCTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATTTAAAA
Found at i:17734 original size:39 final size:38
Alignment explanation
Indices: 17667--17766 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 38
17657 AACATGTTTT
* *
17667 TGAGTATTGTG-ATATGCTTGAATATTATGTGATCATA
1 TGAGTATTGTGAATATGTTTAAATATTATGTGATCATA
* *
17704 TGAGTATTGTGATATATGTTTAAATGTTATGTGATTATA
1 TGAGTATTGTGA-ATATGTTTAAATATTATGTGATCATA
** *
17743 TTTGTAATGTGACATATGTTTAAA
1 TGAGTATTGTGA-ATATGTTTAAA
17767 AGTGAATATG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 11 0.21
39 42 0.79
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (38 bp):
TGAGTATTGTGAATATGTTTAAATATTATGTGATCATA
Found at i:23626 original size:46 final size:46
Alignment explanation
Indices: 23576--23748 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
23566 TGGTTGAGCA
*
23576 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
23622 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
23669 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
23715 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
23749 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:23732 original size:93 final size:93
Alignment explanation
Indices: 23573--23743 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
23563 GGATGGTTGA
* *
23573 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
23638 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
23666 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
23731 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
23744 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:24009 original size:19 final size:20
Alignment explanation
Indices: 23972--24009 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
23962 ATAAGGTGGT
23972 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
23992 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
24010 TGGTGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:31246 original size:89 final size:92
Alignment explanation
Indices: 31093--31258 Score: 223
Period size: 90 Copynumber: 1.8 Consensus size: 92
31083 GGATGGTTGA
* ***
31093 GCATCCGAACTCTTTGAGTTGAGTCCGAGTTCACTTATGGATCAAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCAAACCCCCGAACTCGTTGAGTT
31158 GAGT-CGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
31184 GCATCCGAACT-GTTGAGTTGAGT-GGAGTTCATTTATGGATGCGAACCCCCGAGCTC-TTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-CAAACCCCCGAACTCGTTGAGT
31246 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
31259 ACTTAGGGGC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
89 26 0.40
90 28 0.43
91 11 0.17
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCAAACCCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31518 original size:19 final size:20
Alignment explanation
Indices: 31481--31518 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31471 ATAAGGTGGT
31481 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
31501 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
31519 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Done.