Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2464
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: 39270
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:3479 original size:56 final size:56
Alignment explanation
Indices: 3393--3512 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
3383 ACAAGGGATG
3393 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
3449 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
3505 ATGGGCAA
1 ATGGGCAA
3513 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:4853 original size:80 final size:80
Alignment explanation
Indices: 4639--4862 Score: 278
Period size: 78 Copynumber: 2.8 Consensus size: 80
4629 TCGAATGATG
* * * * *
4639 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
* *
4702 TTGTGCGAGATACTAAT
64 TTGTCCGAGATACTAAA
* *
4719 TCCGGGCTAAG-CCCGAAGGCA-TTGTGTGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
4781 TGTCCGAGTTACTAAA
65 TGTCCGAGATACTAAA
* *
4797 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
4862 G
66 G
4863 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 48 0.39
79 24 0.19
80 48 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTCCGAGATACTAAA
Found at i:4869 original size:40 final size:40
Alignment explanation
Indices: 4639--4862 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
4629 TCGAATGATG
* * * *
4639 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
4679 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
4719 TCCGGGCTAAG-CCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
4757 TCCGGGTTAAGTCCCGAAGGCATTTGTCCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
4797 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
4838 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
4863 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 24 0.15
39 19 0.12
40 108 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:4876 original size:40 final size:40
Alignment explanation
Indices: 4640--4895 Score: 199
Period size: 40 Copynumber: 6.5 Consensus size: 40
4630 CGAATGATGT
* * * * * *
4640 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTAC-GAGTTACTATAA
** * * *
4680 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTACGAGTTACTATA-A
*
4720 CCGGGCTAAG-CCCGAAGGCATTGTGT--GAGTTACTA-AA
1 CCGGGTTAAGTCCCGAAGGCATT-TGTACGAGTTACTATAA
*
4757 TCCGGGTTAAGTCCCGAAGGCATTTGTCCGAGTTACTA-AA
1 -CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
*
4797 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
* * * *
4838 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTA-CTATAA
* *
4878 CC-GGTTAAATTCCGAAGG
1 CCGGGTTAAGTCCCGAAGG
4896 TACGTGATTT
Statistics
Matches: 186, Mismatches: 19, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
38 21 0.11
39 38 0.20
40 117 0.63
41 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
Found at i:10481 original size:27 final size:27
Alignment explanation
Indices: 10443--10497 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
10433 AGTCTAAACA
* *
10443 TCAAAAATCCATAATTTCTGTGAGATT
1 TCAAAAAGCCATAATTTCTGTAAGATT
*
10470 TCAAAAAGCCATAATTTTTGTAAGATT
1 TCAAAAAGCCATAATTTCTGTAAGATT
10497 T
1 T
10498 TTGAGCCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (27 bp):
TCAAAAAGCCATAATTTCTGTAAGATT
Found at i:11971 original size:22 final size:22
Alignment explanation
Indices: 11937--11994 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
11927 TTACTCCAAG
11937 GAAGCC-GATTCATCCATCTCA
1 GAAGCCGGATTCATCCATCTCA
11958 GAAGCCGGATTCATCCATCTCA
1 GAAGCCGGATTCATCCATCTCA
11980 GAAGCCGGATTCATC
1 GAAGCCGGATTCATC
11995 ATCAAGACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (22 bp):
GAAGCCGGATTCATCCATCTCA
Found at i:16046 original size:22 final size:23
Alignment explanation
Indices: 15990--16048 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
15980 GTCCCTAGTC
15990 CACATGGGCGTGTG--CCTCAAT
1 CACATGGGCGTGTGCCCCTCAAT
* * * *
16011 CACACGGCCATGTGCCCCTC-TT
1 CACATGGGCGTGTGCCCCTCAAT
16033 CACATGGGCGTGTGCC
1 CACATGGGCGTGTGCC
16049 TTAGCCACAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 11 0.38
22 14 0.48
23 4 0.14
ACGTcount: A:0.15, C:0.36, G:0.27, T:0.22
Consensus pattern (23 bp):
CACATGGGCGTGTGCCCCTCAAT
Found at i:16072 original size:43 final size:43
Alignment explanation
Indices: 15990--16072 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
15980 GTCCCTAGTC
* * *
15990 CACATGGGCGTGTGCCTCAATCACACGGCCATGTGCCCCTCTT
1 CACATGGGCGTGTGCCTCAACCACACGGCCATATACCCCTCTT
* * *
16033 CACATGGGCGTGTGCCTTAGCCACA-GGACCGTATACCCCT
1 CACATGGGCGTGTGCCTCAACCACACGG-CCATATACCCCT
16073 TCTCATATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
42 2 0.06
43 31 0.94
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.22
Consensus pattern (43 bp):
CACATGGGCGTGTGCCTCAACCACACGGCCATATACCCCTCTT
Found at i:17197 original size:38 final size:39
Alignment explanation
Indices: 17155--17258 Score: 95
Period size: 41 Copynumber: 2.7 Consensus size: 39
17145 AGTTCGAAGC
*
17155 AAAGTTGACACCCAGTGTCTCATCG-GCCTAACCAAAGT
1 AAAGTTGACACCCAGTGTCTCATCGAACCTAACCAAAGT
** ** * * *
17193 AAAG-TGGTACCCAGTACCTCATCGAATCTATCCGAAGT
1 AAAGTTGACACCCAGTGTCTCATCGAACCTAACCAAAGT
*
17231 AAAATAGTGACACCCAGTGTCTCATCGA
1 AAAGT--TGACACCCAGTGTCTCATCGA
17259 CTTGAGGTCG
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
37 16 0.33
38 16 0.33
41 17 0.35
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (39 bp):
AAAGTTGACACCCAGTGTCTCATCGAACCTAACCAAAGT
Found at i:17916 original size:17 final size:18
Alignment explanation
Indices: 17882--17917 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17872 TGAATTTCTA
17882 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
17900 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
17917 T
1 T
17918 AACTCATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:18828 original size:140 final size:142
Alignment explanation
Indices: 18577--18844 Score: 312
Period size: 140 Copynumber: 1.9 Consensus size: 142
18567 AATAAATATC
* * * *
18577 TATTTAATACACAAATACATATATTACAAATGTACACTTATAAATATTTTTACATTTGTATATTA
1 TATTTAATACACAAATACAAATACTACAAATGTACAC-TATAAATATTTTTACATTTGTACAATA
* * * * * * *
18642 TCATGACCATCCATTTATCTTTCTTTTATTTATTTATTATACAAAAATCTTATAATATAATTAAT
65 TCATGACCATACAATTATCATACTTTAATTTATTTACTATACAAAAATCTCATAATATAATTAAT
18707 ATAAATTATAATT
130 ATAAATTATAATT
* * *
18720 TATTTAATA-ACAAATATAAATACTACAATTGTACA-TATATAT-TTTTGTACATTTGTACAATA
1 TATTTAATACACAAATACAAATACTACAAATGTACACTATAAATATTTT-TACATTTGTACAATA
* * *
18782 TCAAT-ACCATACAATTGTCATACTTTCAATTTATTTACTA-ATAAAAATCTCCTAATATAATTA
65 TC-ATGACCATACAATTATCATACTTT-AATTTATTTACTATACAAAAATCTCATAATATAATTA
18845 CTTAATTAGT
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
139 4 0.04
140 57 0.54
141 13 0.12
142 22 0.21
143 9 0.09
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (142 bp):
TATTTAATACACAAATACAAATACTACAAATGTACACTATAAATATTTTTACATTTGTACAATAT
CATGACCATACAATTATCATACTTTAATTTATTTACTATACAAAAATCTCATAATATAATTAATA
TAAATTATAATT
Found at i:22549 original size:18 final size:18
Alignment explanation
Indices: 22520--22564 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
22510 TAAAAAAATA
*
22520 TATTTTTATTATATAA-T
1 TATTTATATTATATAATT
22537 TATTATATATTATATAATT
1 TATT-TATATTATATAATT
22556 TATTTATAT
1 TATTTATAT
22565 AAATAACGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 16 0.64
19 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTATATTATATAATT
Found at i:22604 original size:103 final size:95
Alignment explanation
Indices: 22482--22686 Score: 252
Period size: 95 Copynumber: 2.1 Consensus size: 95
22472 TTTTAAAAAA
* *
22482 TAAAATATATTTAACATAATGATAAATATAAAAAAATATATTTTTATTATATAATTATTATATAT
1 TAAAATATATTTAACATAATGAT--ATAT-AAAAAATATA-TTTTATTATATAATCA-CATAT-T
**
22547 TATATAATTT-ATTTATATAAATAACGGAGTTAGTAATT
60 TAT-T-ATTTGATTT-TATAAATAAAAGAGTTAGTAATT
*
22585 TTAAATAT-TGTTAACATAATGATATATAAAAAATATATTTTATTATATAATCACATATTTATTA
1 TAAAATATAT-TTAACATAATGATATATAAAAAATATATTTTATTATATAATCACATATTTATTA
*
22649 TTTGATTTTATAAATAAAAGAGTTATTAATT
65 TTTGATTTTATAAATAAAAGAGTTAGTAATT
22680 TAAAATA
1 TAAAATA
22687 AAAAAAACTT
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
95 30 0.32
96 5 0.05
97 4 0.04
98 4 0.04
99 15 0.16
100 10 0.11
101 4 0.04
102 1 0.01
103 20 0.22
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (95 bp):
TAAAATATATTTAACATAATGATATATAAAAAATATATTTTATTATATAATCACATATTTATTAT
TTGATTTTATAAATAAAAGAGTTAGTAATT
Found at i:22832 original size:108 final size:110
Alignment explanation
Indices: 22705--22913 Score: 255
Period size: 108 Copynumber: 1.9 Consensus size: 110
22695 TTGAAACAAC
* *
22705 ATGAAATAAAAAAAGTACAAATATGCT-TAGAAGATGAATAAAATCTAG-GACTCAAAGATGAAA
1 ATGAAATAAAAAAAGTACAAATAT-CTGTAGAAGAAGAATAAAA-CTAGAGACTCAAAGATAAAA
* ** *
22768 TCACTATTATTTAACCATCTAACCAAATGAGCTAATATGATAAAAAT
64 CCACTAACATTTAACCATCTAACCAAAGGAGCTAATATGATAAAAAT
* * * * *
22815 ATGAAAT-AAAAAA-TACAAATGTTTGTAGAAGAAGAATCAAACTTGAGACTCAAGGATAAAACC
1 ATGAAATAAAAAAAGTACAAATATCTGTAGAAGAAGAATAAAACTAGAGACTCAAAGATAAAACC
* *
22878 ACTAACATTTAACGATCTAACTAAAGGAGCTAATAT
66 ACTAACATTTAACCATCTAACCAAAGGAGCTAATAT
22914 AACAAAAAAG
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
107 4 0.05
108 67 0.80
109 6 0.07
110 7 0.08
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.24
Consensus pattern (110 bp):
ATGAAATAAAAAAAGTACAAATATCTGTAGAAGAAGAATAAAACTAGAGACTCAAAGATAAAACC
ACTAACATTTAACCATCTAACCAAAGGAGCTAATATGATAAAAAT
Found at i:30462 original size:46 final size:45
Alignment explanation
Indices: 30316--30485 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 45
30306 GGTTGAGCAT
*
30316 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
* * * * * * *
30361 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGATGCAACGC
30405 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
*
30453 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
30486 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
43 2 0.02
44 2 0.02
45 31 0.30
46 63 0.61
47 2 0.02
48 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:37850 original size:46 final size:46
Alignment explanation
Indices: 37800--37971 Score: 213
Period size: 46 Copynumber: 3.7 Consensus size: 46
37790 TGGTTGAGCA
*
37800 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * ** *
37846 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGATGC-AAACG
*
37892 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
37938 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
37972 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
45 2 0.02
46 100 0.96
47 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:37954 original size:92 final size:92
Alignment explanation
Indices: 37797--37966 Score: 304
Period size: 92 Copynumber: 1.8 Consensus size: 92
37787 GGATGGTTGA
* *
37797 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
37862 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
* *
37889 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
37954 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
37967 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Done.