Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1472
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: 52885
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7108 original size:79 final size:82
Alignment explanation
Indices: 6997--7181 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
6987 GCTACTCGTT
* *
6997 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
7060 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
7077 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
7140 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
7157 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
7182 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:7181 original size:40 final size:40
Alignment explanation
Indices: 6978--7181 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
6968 CGGAATTTAA
** *
6978 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7018 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
7058 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7097 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
7137 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
7177 CCGGA
1 CCGGA
7182 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:14909 original size:79 final size:79
Alignment explanation
Indices: 14765--14982 Score: 239
Period size: 79 Copynumber: 2.7 Consensus size: 79
14755 AAATCACGTA
* * * * *
14765 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAG-TACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAG
14829 TAACTCACACAAATG
65 TAACTCACACAAATG
*
14844 CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATA
*
14907 GTATCTCACACAAATG
64 GTAACTCACACAAATG
* * * *
14923 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
14983 CATCATTCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 68 0.57
80 48 0.40
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCACACAAATG
Found at i:14982 original size:40 final size:40
Alignment explanation
Indices: 14798--14982 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
14788 GCTACTCGTT
* *
14798 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
* * **
14838 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
*
14878 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCACA
* * * *
14917 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCA-CA
14958 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
14983 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 80 0.66
41 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
Found at i:21320 original size:193 final size:194
Alignment explanation
Indices: 20991--21376 Score: 695
Period size: 193 Copynumber: 2.0 Consensus size: 194
20981 TTTAAAAATT
20991 TATAACTAATCATTCTTGAAACTAACTATTATCACAATGAAGGCAAGTGTACCTATCGAACAGTA
1 TATAACTAATCATTCTTGAAACTAACTATTATCACAATGAAGGCAAGTGTACCTATCGAACAGTA
* * *
21056 GTATAGCTTAGCAAGACCAGATTGTCGAACCCAAAGGAACCAAGAGTACTCGTAATTACTTTCTT
66 ATATAGCTTAGCAAAACCAGATTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTT
21121 TTTATTATCTAGCCTAAAAATTAAGGGATTT-TTTATCTAAACTAATTAACTAAACTAAGGGTC
131 TTTATTATCTAGCCTAAAAATTAAGGGATTTGTTTATCTAAACTAATTAACTAAACTAAGGGTC
* *
21184 TATAACTAATCGTTCTTGAAACTAACTATTATCACGATGAAGGCAAGTGTACCTATCGAACAGTA
1 TATAACTAATCATTCTTGAAACTAACTATTATCACAATGAAGGCAAGTGTACCTATCGAACAGTA
*
21249 ATATAGCTTTAGCAAAACCAGATTGTCGAACCCAAAGGAACCAATAGTACTAGTAATTACTTT-T
66 ATATAGC-TTAGCAAAACCAGATTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCT
21313 TTTTATTATCTAGCCTAAAAATTAAGGGATTTGTTTATCTAAACTAATTAACTAAACTAAGGGT
130 TTTTATTATCTAGCCTAAAAATTAAGGGATTTGTTTATCTAAACTAATTAACTAAACTAAGGGT
21377 GCACAGAGAG
Statistics
Matches: 185, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
193 102 0.55
194 83 0.45
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (194 bp):
TATAACTAATCATTCTTGAAACTAACTATTATCACAATGAAGGCAAGTGTACCTATCGAACAGTA
ATATAGCTTAGCAAAACCAGATTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTT
TTTATTATCTAGCCTAAAAATTAAGGGATTTGTTTATCTAAACTAATTAACTAAACTAAGGGTC
Found at i:30315 original size:25 final size:25
Alignment explanation
Indices: 30281--30335 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
30271 CTAATTATGA
30281 AAAAGGACTATATCGCATAAAGTGC
1 AAAAGGACTATATCGCATAAAGTGC
30306 AAAAGGACTATATCGCATAAAGTGC
1 AAAAGGACTATATCGCATAAAGTGC
30331 AAAAG
1 AAAAG
30336 TCTTGAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAGGACTATATCGCATAAAGTGC
Found at i:33913 original size:40 final size:40
Alignment explanation
Indices: 33858--34104 Score: 244
Period size: 40 Copynumber: 6.2 Consensus size: 40
33848 CGGATGATAA
* *
33858 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT-T
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-GCTAATAT
* *
33898 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGCTAATAT
*
33938 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGA--GCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTA--ATAT
* *
33978 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGT--TATTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTAATAT
* * *
34016 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGCTAATAT
* *
34057 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-GCTAATAT
34097 CC-GGCTAA
1 CCGGGCTAA
34105 ACTCCGAAGG
Statistics
Matches: 176, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
37 2 0.01
38 3 0.02
39 38 0.22
40 127 0.72
41 5 0.03
42 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTAATAT
Found at i:34114 original size:79 final size:79
Alignment explanation
Indices: 33898--34104 Score: 274
Period size: 79 Copynumber: 2.6 Consensus size: 79
33888 GTGGCTAATT
* *
33898 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* * *
33963 TGCGAGCTATTATAT
65 TGCAAGCTACTATAA
* *
33978 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
34042 TGCAAGTTACTATAA
65 TGCAAGCTACTATAA
* * *
34057 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCCGGGCTAA
34105 ACTCCGAAGG
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 1 0.01
79 73 0.66
80 37 0.33
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCAAGCTACTATAA
Found at i:35822 original size:27 final size:26
Alignment explanation
Indices: 35805--35874 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
35795 ATATTAAGTC
35805 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
35832 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
35860 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
35875 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:35868 original size:28 final size:28
Alignment explanation
Indices: 35805--35902 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
35795 ATATTAAGTC
*
35805 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
35832 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
35860 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
35889 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35903 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:36346 original size:12 final size:12
Alignment explanation
Indices: 36329--36354 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36319 TGGGCATACT
36329 TATGTATATATA
1 TATGTATATATA
36341 TATGTATATATA
1 TATGTATATATA
36353 TA
1 TA
36355 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:43884 original size:39 final size:39
Alignment explanation
Indices: 43840--43935 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
43830 TGGTGAGCTT
43840 CAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTC
1 CAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTC
*
43879 CAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTT
1 CAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTC
* * *
43918 CAGCTAGACTTTGGGCTT
1 CAGTTAGCCTTCGGGCTT
43936 TAGATCCCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (39 bp):
CAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTC
Found at i:51438 original size:46 final size:45
Alignment explanation
Indices: 51388--51559 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 45
51378 TGGTTGAGCA
51388 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
51434 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
51480 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
51526 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
51560 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 96 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:51542 original size:92 final size:92
Alignment explanation
Indices: 51385--51554 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
51375 GGATGGTTGA
* *
51385 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
51450 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
51477 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
51542 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
51555 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Done.