Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_847
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: 44537
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Found at i:589 original size:27 final size:26
Alignment explanation
Indices: 545--596 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
535 CTCGCTGCAA
*
545 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
572 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
597 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:5457 original size:27 final size:26
Alignment explanation
Indices: 5413--5464 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5403 CTCGCTGCAA
*
5413 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
5440 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
5465 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:5532 original size:26 final size:27
Alignment explanation
Indices: 5503--5562 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
5493 CCACATATAT
*
5503 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
5529 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
5556 ATATCTG
1 ATATCTG
5563 GCAGCCTCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:11141 original size:28 final size:28
Alignment explanation
Indices: 11078--11228 Score: 196
Period size: 28 Copynumber: 5.4 Consensus size: 28
11068 GAGATTGGCG
* * * *
11078 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
* *
11107 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
11135 CTAAGTGTGCGAATTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
11163 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
11191 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
11218 CTGAGTCTGCG
1 CTAAGTGTGCG
11229 GACTTAATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
27 23 0.21
28 73 0.66
29 14 0.13
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:18778 original size:17 final size:17
Alignment explanation
Indices: 18756--18792 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
18746 TTAGAGATGA
18756 GTGAATGAAATCGGCAT
1 GTGAATGAAATCGGCAT
18773 GTGAATGAAATCGGCAT
1 GTGAATGAAATCGGCAT
18790 GTG
1 GTG
18793 TGTTTGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.24
Consensus pattern (17 bp):
GTGAATGAAATCGGCAT
Found at i:19372 original size:28 final size:28
Alignment explanation
Indices: 19309--19459 Score: 187
Period size: 28 Copynumber: 5.4 Consensus size: 28
19299 GAGATTGGCG
* * * *
19309 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
* *
19338 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
19366 CTAAGTGTGCGAATTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
19394 CTTAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
19422 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
19449 CTGAGTCTGCG
1 CTAAGTGTGCG
19460 GACTTAATAT
Statistics
Matches: 108, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.21
28 71 0.66
29 14 0.13
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:24042 original size:39 final size:39
Alignment explanation
Indices: 23998--24122 Score: 196
Period size: 39 Copynumber: 3.2 Consensus size: 39
23988 TATGAGATTG
*
23998 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
*
24037 AAAATATCCGGACATGAGGTTCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
* * **
24076 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
24115 AAAATATC
1 AAAATATC
24123 AGGGTTAAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
Found at i:24140 original size:78 final size:76
Alignment explanation
Indices: 23997--24151 Score: 168
Period size: 78 Copynumber: 2.0 Consensus size: 76
23987 GTATGAGATT
* * * ***
23997 GAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGGTTCGCA
1 GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTAGAAAAATATCCGGACATAAGACCCGCA
*
24062 GGCTATATGCTA
66 GGCT-TACGCTA
* * * **
24074 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTAGAAAAATATCAGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGGTCCGCAGGCTACATGCTAGAAAAATATCCGGACAT-AAGACCCG
24138 CAGGCTTACGCTA
64 CAGGCTTACGCTA
24151 G
1 G
24152 TGATGTATTC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
77 12 0.19
78 52 0.81
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTAGAAAAATATCCGGACATAAGACCCGCA
GGCTTACGCTA
Found at i:27494 original size:27 final size:28
Alignment explanation
Indices: 27410--27507 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
27400 CATGAGATTG
* * * *
27410 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
27439 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27467 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27494 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
27508 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27518 original size:27 final size:27
Alignment explanation
Indices: 27438--27520 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
27428 TAAATTGTAC
* *
27438 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
27466 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
27493 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
27520 A
1 A
27521 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:27521 original size:29 final size:27
Alignment explanation
Indices: 27410--27521 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
27400 CATGAGATTG
** * *
27410 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
27439 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
27467 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
27494 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
27522 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:34780 original size:27 final size:28
Alignment explanation
Indices: 34696--34793 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
34686 CATGAGATTG
* * * *
34696 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
34725 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
34753 GCTCTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
34780 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
34794 GACTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.37
28 21 0.34
29 18 0.29
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:34804 original size:27 final size:27
Alignment explanation
Indices: 34724--34806 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
34714 TAAATTGTAC
* *
34724 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
34752 AGCTCTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
34779 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
34806 A
1 A
34807 TTTTGAATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 29 0.60
28 19 0.40
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:34807 original size:29 final size:27
Alignment explanation
Indices: 34696--34807 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 27
34686 CATGAGATTG
** * *
34696 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
34725 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* * *
34753 GCTCTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
34780 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
34808 TTTGAATCAC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
27 22 0.31
28 27 0.39
29 21 0.30
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:40244 original size:12 final size:12
Alignment explanation
Indices: 40227--40259 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40217 CTGCTCCATG
40227 GCCATCTATTTA
1 GCCATCTATTTA
40239 GCCATCTATTTA
1 GCCATCTATTTA
*
40251 GCTATCTAT
1 GCCATCTAT
40260 GCTTTCGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (12 bp):
GCCATCTATTTA
Found at i:42097 original size:15 final size:16
Alignment explanation
Indices: 42064--42097 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42054 TGATAAATTG
*
42064 AAAAATTAAATGCTAA
1 AAAAATTAAATACTAA
*
42080 AAAAATTAAGTACTAA
1 AAAAATTAAATACTAA
42096 AA
1 AA
42098 TTTATAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAAATTAAATACTAA
Found at i:44315 original size:46 final size:46
Alignment explanation
Indices: 44265--44439 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
44255 TGGTTGAGCA
*
44265 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
44311 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
44356 CATCCGAACTCGTTGAGTTGAGTCTG-GTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
44403 -CCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
44440 GCAGGTTACA
Statistics
Matches: 107, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 23 0.21
46 44 0.41
47 26 0.24
49 4 0.04
50 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:44420 original size:92 final size:93
Alignment explanation
Indices: 44262--44431 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
44252 GGATGGTTGA
44262 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
44327 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
44355 GCATCCGAACTCGTTGAGTTGAGTCTG-GTTCACTTATGGATGCGAATG-CCTGAACTCGTTGAG
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
44418 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
44432 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
91 2 0.03
92 47 0.64
93 25 0.34
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Done.