Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2931
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: 49831
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:19748 original size:22 final size:21
Alignment explanation
Indices: 19723--19763 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19713 TTGGATTGTT
*
19723 CACACAGGCGTGTTGCCCCTCC
1 CACACAGGAGTG-TGCCCCTCC
*
19745 CACACGGGAGTGTGCCCCT
1 CACACAGGAGTGTGCCCCT
19764 ATGTCAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.15, C:0.41, G:0.27, T:0.17
Consensus pattern (21 bp):
CACACAGGAGTGTGCCCCTCC
Found at i:23871 original size:21 final size:22
Alignment explanation
Indices: 23839--23880 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
23829 ATGTAATGAG
23839 GTATATTAAGGCCAT-TTAAGA
1 GTATATTAAGGCCATGTTAAGA
23860 GTATAATT-AGGCCATGTTAAG
1 GTAT-ATTAAGGCCATGTTAAG
23881 TGTTATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (22 bp):
GTATATTAAGGCCATGTTAAGA
Found at i:28176 original size:38 final size:38
Alignment explanation
Indices: 28132--28204 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
28122 ATGTTTTTCT
28132 AGCCAAGGACGGTCCAAATGATGATTATTTTATGTTCC
1 AGCCAAGGACGGTCCAAATGATGATTATTTTATGTTCC
28170 AGCCAAGGACGGTCCAAATGATGATTATTTTATGT
1 AGCCAAGGACGGTCCAAATGATGATTATTTTATGT
28205 ACTTTATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (38 bp):
AGCCAAGGACGGTCCAAATGATGATTATTTTATGTTCC
Found at i:35337 original size:51 final size:51
Alignment explanation
Indices: 35260--35509 Score: 405
Period size: 51 Copynumber: 4.9 Consensus size: 51
35250 TGGATACATG
* *
35260 GTGGCCTTCACATAGTACCACCCTTGT-ACGCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTC-CAAAGCTATTTTATTCACAAA
* *
35311 GTGGCATTCACCTAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
35362 GTGGCCTTCACATAGTACTACACTTGTGTCCAAAGCTATTATT-TTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT-TTATTCACAAA
* *
35413 GTGGCCTTCAAATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACGAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
35464 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
35510 CTAATGTACC
Statistics
Matches: 185, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
50 2 0.01
51 180 0.97
52 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:35564 original size:28 final size:24
Alignment explanation
Indices: 35542--35614 Score: 121
Period size: 24 Copynumber: 3.0 Consensus size: 24
35532 ACTTAGCACA
35542 ATGCCATGGA-TATATTTCACTTAG
1 ATGCCATGGACT-TATTTCACTTAG
35566 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
*
35590 ATGCCATGGTCTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
35614 A
1 A
35615 AAAATGTCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 46 0.98
25 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTAG
Found at i:40700 original size:20 final size:20
Alignment explanation
Indices: 40634--40700 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
40624 ATTTTGATAA
*
40634 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40654 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40674 GCATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40694 ACGTGAT
1 ACATGAT
40701 GTTATCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40782 original size:23 final size:24
Alignment explanation
Indices: 40752--40830 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
40742 GGAAGAGAAT
40752 AAGGGCTTATGCCCCAGTTATT-A
1 AAGGGCTTATGCCCCAGTTATTAA
*
40775 AAGGGCTTAGGCCCCAGTTATTAA
1 AAGGGCTTATGCCCCAGTTATTAA
* *
40799 AAGGGCTTTTGCCCCAGTTATTGA
1 AAGGGCTTATGCCCCAGTTATTAA
40823 AAGAGGCT
1 AAG-GGCT
40831 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.42
24 25 0.50
25 4 0.08
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (24 bp):
AAGGGCTTATGCCCCAGTTATTAA
Found at i:40840 original size:25 final size:23
Alignment explanation
Indices: 40752--40840 Score: 108
Period size: 24 Copynumber: 3.7 Consensus size: 23
40742 GGAAGAGAAT
*
40752 AAGGGCTTATGCCCCAGTTATTA
1 AAGGGCTTAGGCCCCAGTTATTA
40775 AAGGGCTTAGGCCCCAGTTATTAA
1 AAGGGCTTAGGCCCCAGTTATT-A
**
40799 AAGGGCTTTTGCCCCAGTTATTGA
1 AAGGGCTTAGGCCCCAGTTATT-A
40823 AAGAGGC-TAGGCCTCCAG
1 AAG-GGCTTAGGCC-CCAG
40841 ATATATGATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.37
24 29 0.51
25 7 0.12
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
AAGGGCTTAGGCCCCAGTTATTA
Found at i:41072 original size:31 final size:31
Alignment explanation
Indices: 41034--41097 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41024 TACCTACAGT
*
41034 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
41065 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41096 AA
1 AA
41098 TTTGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:48583 original size:25 final size:25
Alignment explanation
Indices: 48554--48601 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
48544 TTATAACATG
* * *
48554 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
48579 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
48602 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:48661 original size:18 final size:18
Alignment explanation
Indices: 48640--48688 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
48630 TTTGATATAT
48640 ACATCATGTATGATATGC
1 ACATCATGTATGATATGC
*
48658 ACATGATATGTATGATATGC
1 ACAT--CATGTATGATATGC
*
48678 ACATGATGTAT
1 ACATCATGTAT
48689 CATAAATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 10 0.37
20 17 0.63
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (18 bp):
ACATCATGTATGATATGC
Found at i:48670 original size:20 final size:20
Alignment explanation
Indices: 48645--48684 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
48635 TATATACATC
48645 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAT
48665 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAT
48685 GTATCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
ATGTATGATATGCACATGAT
Found at i:48790 original size:23 final size:23
Alignment explanation
Indices: 48734--48831 Score: 160
Period size: 23 Copynumber: 4.1 Consensus size: 23
48724 AGGAAGTGAA
48734 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
48757 ATTAAGGGCTTATGCCCCAGTTATT
1 A--AAGGGCTTATGCCCCAGTTATT
48782 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
48805 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
48829 AAA
1 AAA
48832 AGAGGCTAGG
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
23 26 0.37
24 22 0.31
25 23 0.32
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:48805 original size:48 final size:47
Alignment explanation
Indices: 48734--48831 Score: 169
Period size: 47 Copynumber: 2.1 Consensus size: 47
48724 AGGAAGTGAA
*
48734 AAAGGGCTTATGCCCCAGTTATTATTAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTTATGCCCCAGTTATT
*
48782 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
48829 AAA
1 AAA
48832 AGAGGCTAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 24 0.50
48 24 0.50
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:48848 original size:25 final size:24
Alignment explanation
Indices: 48733--48852 Score: 172
Period size: 25 Copynumber: 5.0 Consensus size: 24
48723 GAGGAAGTGA
48733 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
48757 ATTAAGGGCTTATGCCCCAGTTATT
1 A-AAAGGGCTTATGCCCCAGTTATT
48782 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
48805 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
48829 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
48853 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
23 22 0.25
24 32 0.37
25 33 0.38
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:49078 original size:30 final size:31
Alignment explanation
Indices: 49044--49106 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
49034 CGTTTACAGT
49044 AAAGGCTTCGGCCCAGTAATATGAAAT-TGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
49074 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
49105 AA
1 AA
49107 TGAAAAGGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Done.