Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold573
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: 74707
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.13
Warning! 44471 characters in sequence are not A, C, G, or T
Found at i:5018 original size:18 final size:19
Alignment explanation
Indices: 4985--5021 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4975 GCCTACGAAC
4985 CAAGTAGAGAACGAACAAG
1 CAAGTAGAGAACGAACAAG
5004 CAAGTAGAG-ACGAACAAG
1 CAAGTAGAGAACGAACAAG
5022 AAGACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.16, G:0.27, T:0.05
Consensus pattern (19 bp):
CAAGTAGAGAACGAACAAG
Found at i:8562 original size:20 final size:20
Alignment explanation
Indices: 8537--8584 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
8527 TCCATGCAGT
* *
8537 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACACCAGCTCAAG
* *
8557 TCAGCTCCCACCAGCTCAAT
1 TCAGCTCACACCAGCTCAAG
8577 TCAGCTCA
1 TCAGCTCA
8585 TTGAGCTCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.21
Consensus pattern (20 bp):
TCAGCTCACACCAGCTCAAG
Found at i:43282 original size:14 final size:14
Alignment explanation
Indices: 43263--43316 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
43253 ACTAGCTCTC
43263 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
43277 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
*
43290 TTTTTTTTCAAAAT
1 TTTTTTTTCACAAT
43304 TTTTTTTTCACAA
1 TTTTTTTTCACAA
43317 CTTGATATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:43371 original size:11 final size:11
Alignment explanation
Indices: 43355--43396 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
43345 GGAAACTAGT
43355 TTTTTTTTGAA
1 TTTTTTTTGAA
43366 TTTTTTTTGAA
1 TTTTTTTTGAA
*
43377 TTTTTTTTCGAG
1 TTTTTTTT-GAA
43389 TTTTTTTT
1 TTTTTTTT
43397 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:43397 original size:12 final size:12
Alignment explanation
Indices: 43352--43400 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
43342 AATGGAAACT
*
43352 AGTTTTTTTTTG
1 AGTTTTTTTTCG
*
43364 AATTTTTTTT-G
1 AGTTTTTTTTCG
*
43375 AATTTTTTTTCG
1 AGTTTTTTTTCG
43387 AGTTTTTTTTCG
1 AGTTTTTTTTCG
43399 AG
1 AG
43401 AAACTACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 11 0.32
12 23 0.68
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.67
Consensus pattern (12 bp):
AGTTTTTTTTCG
Found at i:46326 original size:41 final size:40
Alignment explanation
Indices: 46281--46388 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 40
46271 AATTCGGCCA
* *
46281 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGACACATTTAT
*
46322 AACATGTAGTGGCAGCATTAAATTTGTCCAGACACATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGACACATTTAT
46363 AACATGTAGTGACAGCATTAAATTCG
1 AACATGTAGTG-CAGCATTAAATTCG
46389 ACATATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.02
41 60 0.98
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (40 bp):
AACATGTAGTGCAGCATTAAATTCGTCCAGACACATTTAT
Found at i:46381 original size:22 final size:22
Alignment explanation
Indices: 46316--46381 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 22
46306 GTCCAGGCAT
*
46316 ATTTATAACATGTAGTGGCAGC
1 ATTTATAACATGTAGTGACAGC
** ***
46338 A-TTA-AATTTGTCCAGACA-C
1 ATTTATAACATGTAGTGACAGC
46357 ATTTATAACATGTAGTGACAGC
1 ATTTATAACATGTAGTGACAGC
46379 ATT
1 ATT
46382 AAATTCGACA
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
19 2 0.07
20 11 0.37
21 12 0.40
22 5 0.17
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (22 bp):
ATTTATAACATGTAGTGACAGC
Found at i:48992 original size:11 final size:11
Alignment explanation
Indices: 48976--49001 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48966 ATGTACAAAC
48976 TAAAACATAAT
1 TAAAACATAAT
48987 TAAAACATAAT
1 TAAAACATAAT
48998 TAAA
1 TAAA
49002 TACACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAACATAAT
Found at i:60702 original size:6 final size:6
Alignment explanation
Indices: 60683--60732 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
60673 GGGCTCACAC
** * * *
60683 TCTTTT TCAATT TCTTTT TCTTTT TCCTTT TCCTTT TCTATT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
60731 TC
1 TC
60733 AATTTTATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:66742 original size:50 final size:50
Alignment explanation
Indices: 66667--66909 Score: 335
Period size: 50 Copynumber: 4.8 Consensus size: 50
66657 ATTAGGGTAA
* * *
66667 AGAGGCCCCATGTAAGACCATGTCTGGGACATGGGATTGGCATCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
66717 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA-ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACC-AAGATG
* * *
66767 AGAGGTCCTATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * *
66817 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** *
66867 AGTACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
66910 TGTTATTATC
Statistics
Matches: 172, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 135 0.78
51 36 0.21
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Done.