Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3052
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: 35988
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Found at i:1830 original size:29 final size:29
Alignment explanation
Indices: 1792--1865 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
1782 CGGTTGAGAT
* *
1792 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
1821 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
1850 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
1866 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:10143 original size:29 final size:29
Alignment explanation
Indices: 10108--10181 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
10098 GTTGTGAGAT
* *
10108 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
10137 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
10166 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
10182 TGGTTGTTAT
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:12632 original size:11 final size:11
Alignment explanation
Indices: 12616--12645 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
12606 TTTAAAGTAT
12616 ATTATTTTTAA
1 ATTATTTTTAA
12627 ATTA-TTTTAA
1 ATTATTTTTAA
12637 ATTATTTTT
1 ATTATTTTT
12646 TTTGTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTATTTTTAA
Found at i:20358 original size:46 final size:46
Alignment explanation
Indices: 20206--20560 Score: 208
Period size: 46 Copynumber: 7.5 Consensus size: 46
20196 TTTGTGTGCT
* * * * *
20206 AGTGTAAGACATTTCTGGGACATGCATCAGCCAC-ATTATGTGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTAAGCC
* * * * *
20252 AGTGTAAGACCATGTCTGGGACCTAGCATTGGTACT-GAGACG-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CCTCGAGATGTA-AGCC
* *
20300 AATGTAAGACATGTGTGGGACATGCATCGGCCTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
* * *
20346 AGTGTAAGACATGTCTGGGACATGCATTGG-CTATGAGATGT--GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGCC
** * *
20390 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAAGT--GTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-C-TCGAGATGTAAGCC
* * * * *
20438 AGTGTAAGACCATGCCTAGGACATGGCATCGG-CACGACTATGTGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA-GATGT-A-AGCC
* ** *
20488 AGTGTAAGACCATGTCTGGGACATGACGTCGGCCTCGATTTCG-ATAGTC
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCGAGAT-GTA-AGCC
20537 AGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGA-CATGTCTGGGACAT
20561 CACATCGACT
Statistics
Matches: 245, Mismatches: 43, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
44 11 0.04
45 19 0.08
46 67 0.27
47 25 0.10
48 57 0.23
49 31 0.13
50 30 0.12
51 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
Found at i:20447 original size:48 final size:48
Alignment explanation
Indices: 20345--20613 Score: 200
Period size: 48 Copynumber: 5.6 Consensus size: 48
20335 AGATGTAAGC
* *
20345 CAGTGTAAGA-CATGTCTGGGACATG-CAT-TG-GC-TATGAGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGACATCGGCGCGTAT-AGAAGTGT
*
20389 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAAGTGT
1 CAGTGTAAGACCATGTCTGGGACATGACATCGGCGCGTATAGAAGTGT
* * * * * *
20437 CAGTGTAAGACCATGCCTAGGACATGGCATCGGCACG-ACTATGTGAGAG-
1 CAGTGTAAGACCATGTCTGGGACATGACATCGGCGCGTA-TA-G-AAGTGT
* * * *
20486 CTAGTGTAAGACCATGTCTGGGACATGACGTCGGCCTCGATTTCG-A-TAGT
1 C-AGTGTAAGACCATGTCTGGGACATGACATCGG-CGCG-TATAGAAGT-GT
* * ** * * *
20536 CAGTGTAAGACCATGTCTGGGACATCACATCGACTTG-ATAGATGAGC
1 CAGTGTAAGACCATGTCTGGGACATGACATCGGCGCGTATAGAAGTGT
20583 CAGTGTAAGACCATGT-TCGGGACATGACATC
1 CAGTGTAAGACCATGTCT-GGGACATGACATC
20614 AACATTGTAC
Statistics
Matches: 183, Mismatches: 25, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
44 10 0.05
45 15 0.08
46 6 0.03
47 31 0.17
48 48 0.26
49 36 0.20
50 32 0.17
51 4 0.02
52 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGACATCGGCGCGTATAGAAGTGT
Found at i:22266 original size:17 final size:17
Alignment explanation
Indices: 22244--22276 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
22234 AAAAATGTAG
22244 GCTGATATGAGTACTAC
1 GCTGATATGAGTACTAC
22261 GCTGATATGAGTACTA
1 GCTGATATGAGTACTA
22277 ATAATATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (17 bp):
GCTGATATGAGTACTAC
Found at i:24682 original size:26 final size:26
Alignment explanation
Indices: 24644--24698 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
24634 ACAAGTTAGC
24644 AAAGAAAGCCTTTGTGGCATAATATG
1 AAAGAAAGCCTTTGTGGCATAATATG
* **
24670 AAAGAAAGTCTTTGTGGTGTAATATG
1 AAAGAAAGCCTTTGTGGCATAATATG
24696 AAA
1 AAA
24699 AAAAATTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (26 bp):
AAAGAAAGCCTTTGTGGCATAATATG
Found at i:25990 original size:33 final size:33
Alignment explanation
Indices: 25948--26014 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
25938 GTGGAAAAAG
25948 TAAGGTTATCGAGTAATCGATCTGATTTGTCAA
1 TAAGGTTATCGAGTAATCGATCTGATTTGTCAA
25981 TAAGGTTATCGAGTAATCGATCTGATTTGTCAA
1 TAAGGTTATCGAGTAATCGATCTGATTTGTCAA
26014 T
1 T
26015 TTCGAGTACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (33 bp):
TAAGGTTATCGAGTAATCGATCTGATTTGTCAA
Done.