Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3798
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: 44364
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6308 original size:40 final size:40
Alignment explanation
Indices: 6248--6471 Score: 288
Period size: 40 Copynumber: 5.5 Consensus size: 40
6238 TATTCGGATG
6248 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
6288 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
6331 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
6371 ATATCCGAGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
6411 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
6451 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
6472 ATACTTGGGT
Statistics
Matches: 161, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 13 0.08
40 111 0.69
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:6391 original size:83 final size:79
Alignment explanation
Indices: 6252--6471 Score: 282
Period size: 83 Copynumber: 2.7 Consensus size: 79
6242 CGGATGATAT
* * **
6252 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATTCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATA-TCCGGCTAAGTCCCGAAGGCATTCA
6317 TGCGAGTAGTTG-CTATAC
65 TGC---TAG-TGACTATAC
*
6335 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGAGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCG-GCTAAGTCCCGAAGGCATTCA
*
6400 TGCTAGTGACTATAT
65 TGCTAGTGACTATAC
* * *
6415 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGCTAAGTCCCGAAG
6472 ATACTTGGGT
Statistics
Matches: 125, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
79 15 0.12
80 46 0.37
81 2 0.02
82 3 0.02
83 59 0.47
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGCTAAGTCCCGAAGGCATTCAT
GCTAGTGACTATAC
Found at i:8364 original size:43 final size:44
Alignment explanation
Indices: 8295--8397 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 44
8285 CCGGACAGGA
* * * * * *
8295 TCTTACACGAAATCA-TATAACGATGCCAATTTCCTACACATGG
1 TCTTACACGTAATCACAATAACAATGCCAATGTCCCACACATAG
* *
8338 TCTTACACGTAATCACAAT-ACAATGCCAATGTCCCAGACGTAG
1 TCTTACACGTAATCACAATAACAATGCCAATGTCCCACACATAG
*
8381 TCTTACATGTAATCACA
1 TCTTACACGTAATCACA
8398 TCTCAATAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 48 0.96
44 2 0.04
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (44 bp):
TCTTACACGTAATCACAATAACAATGCCAATGTCCCACACATAG
Found at i:14909 original size:40 final size:40
Alignment explanation
Indices: 14835--15056 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
14825 AACCCAAGTA
* * *
14835 CCTTCGGAATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
14874 CCTTTGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
14914 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
14954 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * ** *
14994 CCTTCAGGACTTAGCCCAGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
15034 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
15057 CATCCGAATA
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
39 10 0.06
40 154 0.93
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:24759 original size:21 final size:21
Alignment explanation
Indices: 24733--24788 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
24723 CACTAGACAT
*
24733 AGGGGCACATGCCCATATGAA
1 AGGGGCACACGCCCATATGAA
* *
24754 AGGGGCATACGCCCATGTGAA
1 AGGGGCACACGCCCATATGAA
24775 AGGGGCACACGCCC
1 AGGGGCACACGCCC
24789 GTGTAGCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.11
Consensus pattern (21 bp):
AGGGGCACACGCCCATATGAA
Found at i:34563 original size:47 final size:47
Alignment explanation
Indices: 34456--34793 Score: 525
Period size: 47 Copynumber: 7.1 Consensus size: 47
34446 GAAATGATAG
34456 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
34505 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
34552 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
34599 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
34650 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
34696 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * *
34743 CAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
34790 TAAG
1 TAAG
34794 TCCCGAAGGG
Statistics
Matches: 269, Mismatches: 15, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
46 12 0.04
47 176 0.65
49 36 0.13
50 34 0.13
51 11 0.04
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:34715 original size:144 final size:145
Alignment explanation
Indices: 34456--34782 Score: 552
Period size: 144 Copynumber: 2.3 Consensus size: 145
34446 GAAATGATAG
34456 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGC
34519 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
66 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
34584 AGCGTATATATGAGA
131 AGCGTATATATGAGA
34599 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGAT-AGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGC
*
34663 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
66 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
34728 AGTGTATATATGTGA
131 AGCGTATATATGAGA
* * * * * *
34743 CAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
34783 AATGTGATAA
Statistics
Matches: 173, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
143 36 0.21
144 123 0.71
145 14 0.08
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (145 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGC
CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGCGTATATATGAGA
Found at i:34968 original size:37 final size:37
Alignment explanation
Indices: 34912--34990 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
34902 CCGAGCTCTA
* * *
34912 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
34949 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
34986 AAGAC
1 AAGAC
34991 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:36930 original size:29 final size:29
Alignment explanation
Indices: 36895--36968 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
36885 GTTGTGAGAT
* *
36895 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
36924 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
36953 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
36969 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:37381 original size:39 final size:40
Alignment explanation
Indices: 37280--37423 Score: 154
Period size: 40 Copynumber: 3.6 Consensus size: 40
37270 TCGAATGATG
* *
37280 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
37319 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
37360 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
37399 TCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAG-GCATT
37424 CATGCTAGTG
Statistics
Matches: 90, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
39 35 0.39
40 37 0.41
41 17 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:37442 original size:40 final size:40
Alignment explanation
Indices: 37360--37514 Score: 163
Period size: 40 Copynumber: 3.9 Consensus size: 40
37350 AGATACTAAT
** * *
37360 TCCGGGCTAAG-CCCGAAG-GCATTGGTGC-GAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTG-GTGA-TATA
* *
37399 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATATA
* * *
37439 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATATA
* * *
37479 TCCTGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGA
37515 CGTGTATTCG
Statistics
Matches: 96, Mismatches: 17, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
39 11 0.11
40 74 0.77
41 11 0.11
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATATA
Found at i:41456 original size:47 final size:47
Alignment explanation
Indices: 41349--41681 Score: 512
Period size: 47 Copynumber: 7.1 Consensus size: 47
41339 GAAATGATAG
41349 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
41398 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41445 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA---GA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41489 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
41538 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41585 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
41632 -CAGGGCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41678 TAAG
1 TAAG
41682 TCCCGAAGGG
Statistics
Matches: 266, Mismatches: 12, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
44 38 0.14
46 44 0.17
47 111 0.42
49 73 0.27
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41601 original size:140 final size:139
Alignment explanation
Indices: 41345--41681 Score: 552
Period size: 140 Copynumber: 2.4 Consensus size: 139
41335 ATATGAAATG
41345 ATAGTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
1 ATAGTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
41410 GCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
66 GCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
41475 AAAGTGTAT
131 AAAGTGTAT
*
41484 ATAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAAT
1 ATAG-TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
*
41549 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65 GGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGT
41614 GAAAGTGTAT
130 GAAAGTGTAT
* * * * * *
41624 ATATGTGACAGGGCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATA-GT-A-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
41682 TCCCGAAGGG
Statistics
Matches: 185, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
139 4 0.02
140 146 0.79
141 3 0.02
142 32 0.17
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (139 bp):
ATAGTAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
GCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
AAAGTGTAT
Found at i:41867 original size:37 final size:35
Alignment explanation
Indices: 41800--41876 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 35
41790 CCGAGCTCTA
* * *
41800 AAGACCCGATGACTGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTGTGTGGAGATTATGTCCGGGT
41835 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAAC-T-GTGTGGAGATTATGTCCGGGT
41872 AAGAC
1 AAGAC
41877 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 12 0.32
36 1 0.03
37 24 0.65
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (35 bp):
AAGACCCGATAACTGTGTGGAGATTATGTCCGGGT
Done.