Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold406
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: 36239
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Found at i:7612 original size:40 final size:40
Alignment explanation
Indices: 7533--7775 Score: 339
Period size: 40 Copynumber: 6.1 Consensus size: 40
7523 CGAGATTTAA
* *
7533 CCGGATATAGCT-ACTCGCTC-AATGCCTTCGGGACGTAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
7572 CCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
7612 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7652 CCGGATGTAATAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
7692 CCGGATGTAATAACTCGCACAAATGCCTTCGAGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
7732 CC-GAAACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
7772 CCGG
1 CCGG
7776 TTATCATCCG
Statistics
Matches: 187, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 19 0.10
40 166 0.89
41 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12252 original size:48 final size:46
Alignment explanation
Indices: 12134--12252 Score: 134
Period size: 46 Copynumber: 2.5 Consensus size: 46
12124 AGTTATATGT
* *
12134 AAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGACGA
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGA
* * *
12180 AAGCTAGTGTAAGACATGTTTGGGACATGCATC-AGCCTT-AGGATATA
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCGA-CATTGA-GA-AGA
*
12227 CAAGCTAGTGTAAGACTTGTCTGGGA
1 -AAGCTAGTGTAAGACATGTCTGGGA
12253 TATGGCGTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 2 0.03
46 36 0.58
47 1 0.02
48 23 0.37
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (46 bp):
AAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGA
Found at i:13703 original size:21 final size:20
Alignment explanation
Indices: 13678--13717 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
13668 GTCAATAGGG
13678 CCACACGGGCATGTTGCCCTT
1 CCACACGGGCATGTT-CCCTT
*
13699 CCACACGGGCGTGTTCCCT
1 CCACACGGGCATGTTCCCT
13718 GTTTTAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.40, G:0.25, T:0.23
Consensus pattern (20 bp):
CCACACGGGCATGTTCCCTT
Found at i:15750 original size:32 final size:32
Alignment explanation
Indices: 15713--15773 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
15703 TGAAAACGAG
**
15713 GATGTTCTTTGGGTTGAATCGAGTAGAACGGA
1 GATGTTCTTCAGGTTGAATCGAGTAGAACGGA
*
15745 GATGTTCTTCAGGTTGAATCGGGTAGAAC
1 GATGTTCTTCAGGTTGAATCGAGTAGAAC
15774 AGATAACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.31
Consensus pattern (32 bp):
GATGTTCTTCAGGTTGAATCGAGTAGAACGGA
Found at i:18372 original size:37 final size:37
Alignment explanation
Indices: 18313--18421 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
18303 AGCTCAGACG
* * *
18313 AAATCTCCACACGAAGTTATCGGGTCTTACCCTGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
18350 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
18387 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
18422 ATGTATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:18622 original size:48 final size:47
Alignment explanation
Indices: 18568--18948 Score: 564
Period size: 48 Copynumber: 7.8 Consensus size: 47
18558 GCACATCGCC
18568 TACATATTTCACACTATCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTA-CCATTCGGCTTTACCACATATACATATCTCA
18616 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTA-CCATTCGGCTTTACCACATATACATATCTC--A
* *
18666 TATATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACT-ACCATTCGGCTTTACCACATATACATATCTCA
18714 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTA-CCATTCGGCTTTACCACATATACATATCTC--A
* *
18764 TATATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACT-ACCATTCGGCTTTACCACATATACATATCTCA
18812 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTA-CCATTCGGCTTTACCACATATACATATCTC--A
* * *
18862 TATATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACACT-ACCATTCGGCTTTACCACATATACATATCTCA
*
18910 TACATATTTCACATTATCCATTCGGCTTTACCACATATA
1 TACATATTTCACACTA-CCATTCGGCTTTACCACATATA
18949 TGCATGTTCA
Statistics
Matches: 307, Mismatches: 14, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
47 3 0.01
48 170 0.55
50 131 0.43
51 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (47 bp):
TACATATTTCACACTACCATTCGGCTTTACCACATATACATATCTCA
Found at i:18721 original size:98 final size:98
Alignment explanation
Indices: 18571--18948 Score: 704
Period size: 98 Copynumber: 3.9 Consensus size: 98
18561 CATCGCCTAC
*
18571 ATATTTCACACT-ATCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCC
1 ATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCC
18635 ATTCGGCTTTACCACATATACATATCTCATATAT
65 ATTCGGCTTTACCACATATACATATCTCATATAT
18669 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
18734 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
18767 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
18832 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
* * *
18865 ATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCATACATATTTCACATTATCCA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
18930 TTCGGCTTTACCACATATA
66 TTCGGCTTTACCACATATA
18949 TGCATGTTCA
Statistics
Matches: 275, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
98 274 1.00
99 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (98 bp):
ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
TTCGGCTTTACCACATATACATATCTCATATAT
Found at i:18990 original size:22 final size:22
Alignment explanation
Indices: 18964--19082 Score: 66
Period size: 22 Copynumber: 5.1 Consensus size: 22
18954 GTTCATATTC
18964 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
18986 ATCACACATGTG-CATGCTC-ACATT
1 ATCACA-TTG-GCCAT--TCGGCCTT
19010 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
19033 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
19057 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
19080 ATC
1 ATC
19083 TCATATATAC
Statistics
Matches: 71, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
22 21 0.30
23 16 0.23
24 16 0.23
25 18 0.25
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:19000 original size:47 final size:47
Alignment explanation
Indices: 18918--19111 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
18908 CATACATATT
** * * *
18918 TCACATTATCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
18965 TCACATTGGCCATTCGGCCTTATCACACATGTGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19012 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
19059 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19106 TCACAT
1 TCACAT
19112 AAAATCCTAA
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:23205 original size:27 final size:27
Alignment explanation
Indices: 23175--23348 Score: 197
Period size: 27 Copynumber: 6.4 Consensus size: 27
23165 TGAGTCCGCT
* * * *
23175 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
23202 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
23229 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
23257 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
23284 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
23311 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
23338 CACTTAGTGCT
1 CACTTAGTGCT
23349 GTACAATTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:23317 original size:82 final size:81
Alignment explanation
Indices: 23192--23347 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
23182 TGCTATATAA
* *
23192 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
23257 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
23274 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
23338 CACTTAGTGC
65 CACTTAGTGC
23348 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31265 original size:28 final size:27
Alignment explanation
Indices: 31200--31378 Score: 173
Period size: 27 Copynumber: 6.6 Consensus size: 27
31190 ATATTGAGTC
* * *
31200 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
31227 CGCACACTTAGTGCTACGTAATCCAAAT
1 CGCACACTTAGTGCTACATAAT-CAAAT
*
31255 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
31283 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
31310 CGCACAC-TAGTGC-ATCAATATTCATTT
1 CGCACACTTAGTGCTA-C-ATAATCAAAT
* *
31337 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
31364 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31379 GTAACAATTT
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.05
27 66 0.52
28 54 0.42
29 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:31313 original size:55 final size:54
Alignment explanation
Indices: 31200--31378 Score: 191
Period size: 55 Copynumber: 3.3 Consensus size: 54
31190 ATATTGAGTC
* * * * *
31200 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGT-CAAAT
* ** * *
31255 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
31310 CGCACAC-TAGTGC-ATCAATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-C-ATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
31364 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31379 GTAACAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 39 0.38
55 42 0.41
56 21 0.20
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:34452 original size:39 final size:38
Alignment explanation
Indices: 34353--34626 Score: 258
Period size: 39 Copynumber: 6.9 Consensus size: 38
34343 TACACCAGCA
34353 ACGAATGCTTCTTCGGAACTTAGCCCAGGATACATC-CTAGC
1 ACGAATGC-TCTTCGG-ACTTAG-CC-GGATACATCACTAGC
*
34394 ACGAATTTGCTC-TCGGACTTAAGCCGGATATATCACTAGC
1 ACGAA--TGCTCTTCGGACTT-AGCCGGATACATCACTAGC
*
34434 ACGAATGCTCTTCAGACTTAGCCCGGATACATCACTAGC
1 ACGAATGCTCTTCGGACTTAG-CCGGATACATCACTAGC
*
34473 ACCGAATGCTCTTTCAGG-CTTAGCCAG-TACATCACTAGC
1 A-CGAATGCTC-TTC-GGACTTAGCCGGATACATCACTAGC
*
34512 ACGAATGCTCTTCGCGGACTTAGCCCGGCA-ATGATCACTAGC
1 ACGAATGCTCTT--CGGACTTAG-CCGG-ATA-CATCACTAGC
* *
34554 ACGAATGCGCTTCGGGACTTAGCCCGA-ACATCACTAGC
1 ACGAATGCTCTTC-GGACTTAGCCGGATACATCACTAGC
*
34592 -CGAATGCCTCTT-GTACTTTAGCCGGATACATCACT
1 ACGAATG-CTCTTCGGAC-TTAGCCGGATACATCACT
34627 CTCAATTCTC
Statistics
Matches: 200, Mismatches: 13, Indels: 43
0.78 0.05 0.17
Matches are distributed among these distances:
36 3 0.01
37 16 0.08
38 39 0.19
39 53 0.26
40 35 0.17
41 28 0.14
42 23 0.12
43 3 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (38 bp):
ACGAATGCTCTTCGGACTTAGCCGGATACATCACTAGC
Found at i:34507 original size:78 final size:77
Alignment explanation
Indices: 34353--34626 Score: 269
Period size: 80 Copynumber: 3.5 Consensus size: 77
34343 TACACCAGCA
34353 ACGAATGCTTCTTCGGAACTTAGCCCAGGATACATC-CTAGCACGAATTTGCTC-TCGGACTTAA
1 ACGAATGC-TCTTCGGAACTTAGCCC-GGATACATCACTAGCACGAA--TGCTCTTCGGACTT-A
* *
34416 GCCGGATATATCACTAGC
61 GCCAG-TACATCACTAGC
*
34434 ACGAATGCTCTTCAG-ACTTAGCCCGGATACATCACTAGCACCGAATGCTCTTTCAGG-CTTAGC
1 ACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCA-CGAATGCTC-TTC-GGACTTAGC
34497 CAGTACATCACTAGC
63 CAGTACATCACTAGC
* * *
34512 ACGAATGCTCTTCGCGGACTTAGCCCGGCA-ATGATCACTAGCACGAATGCGCTTCGGGACTTAG
1 ACGAATGCTCTTCG-GAACTTAGCCCGG-ATA-CATCACTAGCACGAATGCTCTTC-GGACTTAG
* *
34576 CCCGAACATCACTAGC
62 CCAGTACATCACTAGC
*
34592 -CGAATGCCTCTT--GTACTTTAG-CCGGATACATCACT
1 ACGAATG-CTCTTCGGAAC-TTAGCCCGGATACATCACT
34627 CTCAATTCTC
Statistics
Matches: 169, Mismatches: 11, Indels: 31
0.80 0.05 0.15
Matches are distributed among these distances:
76 7 0.04
77 8 0.05
78 42 0.25
79 32 0.19
80 59 0.35
81 21 0.12
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (77 bp):
ACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCAG
TACATCACTAGC
Done.