Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1839
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: 25630
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Found at i:4506 original size:102 final size:103
Alignment explanation
Indices: 4331--4592 Score: 426
Period size: 102 Copynumber: 2.6 Consensus size: 103
4321 TAACCGTTAT
* *
4331 TGGTGGATCTCGCACTTAGCACCACCACTGAAT-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
4395 AATCAGCACATAGCAACCCCCTTT-CATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTACATTTCAAAGATA
4432 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
4497 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATA
* **
4536 TGGTGGATCA-CGCACATAGCACCACCAA--AATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
4593 TTTATATACA
Statistics
Matches: 152, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
101 31 0.20
102 82 0.54
104 38 0.25
105 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTACATTTCAAAGATA
Found at i:4949 original size:29 final size:29
Alignment explanation
Indices: 4916--4979 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
4906 TAATCCACCA
4916 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
4945 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
4975 CCCAA
1 CCCAA
4980 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:4953 original size:30 final size:30
Alignment explanation
Indices: 4923--4979 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4913 CCACCCAACT
4923 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
4952 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
4980 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:11866 original size:26 final size:26
Alignment explanation
Indices: 11836--11887 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11826 CACCACTGAA
*
11836 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
11862 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
11888 CTTTTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:11968 original size:26 final size:26
Alignment explanation
Indices: 11938--11989 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11928 CACCAATGAA
*
11938 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
11964 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
11990 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:11981 original size:102 final size:103
Alignment explanation
Indices: 11805--12067 Score: 440
Period size: 102 Copynumber: 2.6 Consensus size: 103
11795 AACCGTTATT
* *
11805 GGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
*
11870 TCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
11907 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
*
11972 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
12010 GGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
12068 TTTATATACA
Statistics
Matches: 152, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
102 85 0.56
103 66 0.43
104 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:12429 original size:29 final size:29
Alignment explanation
Indices: 12396--12459 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
12386 TAATCCACCA
12396 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
12425 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
12455 CCCAA
1 CCCAA
12460 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:12433 original size:30 final size:30
Alignment explanation
Indices: 12403--12459 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12393 CCACCCAACT
12403 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
12432 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
12460 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:14698 original size:63 final size:63
Alignment explanation
Indices: 14599--14725 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
14589 AGGCCGCCTC
**
14599 GGATAGACAGAAATCTTACGTGGATTTGAAACGAAAGGAAATTGAATTTCAAGTCGGCAATAA
1 GGATAGACAGAAATCTTACGCAGATTTGAAACGAAAGGAAATTGAATTTCAAGTCGGCAATAA
*
14662 GGATAGATAGAAATCTTACGCAGATTTGAAACGAAAGGAAATTGAATTTCAAGTCGGCAATAA
1 GGATAGACAGAAATCTTACGCAGATTTGAAACGAAAGGAAATTGAATTTCAAGTCGGCAATAA
14725 G
1 G
14726 TTATTTTTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (63 bp):
GGATAGACAGAAATCTTACGCAGATTTGAAACGAAAGGAAATTGAATTTCAAGTCGGCAATAA
Found at i:16528 original size:46 final size:45
Alignment explanation
Indices: 16384--16551 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 45
16374 ATTGTGAGCT
* * * *
16384 AGTGTCAGACATGTCTGGGACATGCATCGGCCACATTATGA-GAA-CC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTC--GA-GACGAAGCC
* * * * *
16430 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGACGA-AGCC
16478 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACG-AAGCC
* *
16524 AGTGTAAGACATGTCTAGGACTTGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
16552 GGCTATGAGA
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.02
46 53 0.52
47 29 0.28
48 18 0.18
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGAAGCC
Found at i:20415 original size:78 final size:81
Alignment explanation
Indices: 20272--20455 Score: 234
Period size: 78 Copynumber: 2.3 Consensus size: 81
20262 GCTACTCGTT
* *
20272 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
20337 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* * **
20352 CAAATGCCTTCGGG-CTTAACCCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
20414 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
20431 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20456 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
77 3 0.03
78 46 0.51
79 27 0.30
80 14 0.16
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:20455 original size:40 final size:40
Alignment explanation
Indices: 20253--20455 Score: 236
Period size: 40 Copynumber: 5.1 Consensus size: 40
20243 CGGAATTTAA
** *
20253 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20293 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20333 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20372 CCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
20411 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
20451 CCGGA
1 CCGGA
20456 CATCATTCAA
Statistics
Matches: 142, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
37 2 0.01
38 22 0.15
39 23 0.16
40 84 0.59
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.