Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold165
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: 1947055
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.31
Warning! 52078 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1920937 original size:12 final size:12
Alignment explanation
Indices: 1920873--1920942 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
1920863 ATTTTTTATA
1920873 TTAATATTTATAA-
1 TTAA-ATTT-TAAT
1920886 TTAAATTTTAAT
1 TTAAATTTTAAT
*
1920898 TTAAA-TTAAAT
1 TTAAATTTTAAT
*
1920909 TAAAATTTTTATTAT
1 TTAAA-TTTTA--AT
*
1920924 TTAAATATTAAT
1 TTAAATTTTAAT
1920936 TTAAATT
1 TTAAATT
1920943 AAAATAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
11 12 0.26
12 17 0.37
13 7 0.15
14 4 0.09
15 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAATTTTAAT
Found at i:1920943 original size:21 final size:21
Alignment explanation
Indices: 1920886--1921028 Score: 57
Period size: 20 Copynumber: 7.2 Consensus size: 21
1920876 ATATTTATAA
* *
1920886 TTAAATTTTAATTTAAATTAAA
1 TTAAATATTAATTTAAATT-AT
1920908 TTAAA-ATT--TTT--ATTAT
1 TTAAATATTAATTTAAATTAT
1920924 TTAAATATTAATTTAAATTA-
1 TTAAATATTAATTTAAATTAT
1920944 --AAATAAATTAATTTAAA--A-
1 TTAAAT--ATTAATTTAAATTAT
1920962 TTATAATAATTATATTTAAAATTAAT
1 TTA-AAT-ATTA-ATTT-AAATT-AT
* * *
1920988 TT-AATA-TAAATTAATTTTT
1 TTAAATATTAATTTAAATTAT
1921007 TTAAAT-TTAA--TAAATTAT
1 TTAAATATTAATTTAAATTAT
1921025 TTAA
1 TTAA
1921029 TTTATGAATA
Statistics
Matches: 96, Mismatches: 7, Indels: 40
0.67 0.05 0.28
Matches are distributed among these distances:
16 6 0.06
17 6 0.06
18 15 0.16
19 9 0.09
20 27 0.28
21 16 0.17
22 10 0.10
23 1 0.01
24 3 0.03
25 1 0.01
26 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATATTAATTTAAATTAT
Found at i:1920959 original size:15 final size:15
Alignment explanation
Indices: 1920922--1921004 Score: 53
Period size: 15 Copynumber: 5.3 Consensus size: 15
1920912 AATTTTTATT
*
1920922 ATTTAAATATTAATTTA
1 ATTTAAA-A-TAAATTA
*
1920939 AATTAAAATAAATTA
1 ATTTAAAATAAATTA
1920954 ATTTAAAATTATAA-TA
1 ATTTAAAA-TA-AATTA
**
1920970 A-TTATATTTAAAATTA
1 ATTTA-AAAT-AAATTA
*
1920986 ATTTAATATAAATTA
1 ATTTAAAATAAATTA
1921001 ATTT
1 ATTT
1921005 TTTTAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
15 29 0.54
16 14 0.26
17 11 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAAATAAATTA
Found at i:1921039 original size:90 final size:91
Alignment explanation
Indices: 1920874--1921042 Score: 202
Period size: 90 Copynumber: 1.9 Consensus size: 91
1920864 TTTTTTATAT
* * * *
1920874 TAATATTTATAATTAAATTTTAATTTAAATTAAATTAAAATTTTTATTATTTAAATATTAATTTA
1 TAATAATTATAATTAAATATTAATTTAAATTAAATTAAAATTTTTATAATTTAAAAATTAATTTA
1920939 AATTAAAATAAATTAATTTAAAATTA
66 AATTAAAATAAATTAATTTAAAATTA
* **
1920965 TAATAATTATATTTAAA-ATTAATTT-AATATAAATTAATTTTTTTA-AATTTAATAAATT-ATT
1 TAATAATTATAATTAAATATTAATTTAAAT-TAAATTAAAATTTTTATAATTTAA-AAATTAATT
* *
1921026 TAATTTATGAATAAATT
64 TAAATTA-AAATAAATT
1921043 TATTGAGTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
89 18 0.27
90 33 0.50
91 15 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (91 bp):
TAATAATTATAATTAAATATTAATTTAAATTAAATTAAAATTTTTATAATTTAAAAATTAATTTA
AATTAAAATAAATTAATTTAAAATTA
Found at i:1922311 original size:15 final size:15
Alignment explanation
Indices: 1922275--1922339 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
1922265 AATTTTCCCA
*
1922275 TTATTTTTTATT-TT
1 TTATTTTTAATTATT
1922289 TT-TCTTTTAATTATT
1 TTAT-TTTTAATTATT
1922304 TTATTTTTGTATATTATT
1 TTA-TTTT-TA-ATTATT
* *
1922322 TTATTTTTTATTACT
1 TTATTTTTAATTATT
1922337 TTA
1 TTA
1922340 CTCGTATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 1 0.02
14 9 0.21
15 12 0.29
16 4 0.10
17 7 0.17
18 9 0.21
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (15 bp):
TTATTTTTAATTATT
Found at i:1922339 original size:8 final size:8
Alignment explanation
Indices: 1922274--1922339 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
1922264 AAATTTTCCC
1922274 ATTATTTT
1 ATTATTTT
1922282 -TTATTTT
1 ATTATTTT
* *
1922289 TTTCTTTT
1 ATTATTTT
1922297 AATTATTTT
1 -ATTATTTT
*
1922306 ATTTTTGTAT
1 ATTATT-T-T
1922316 ATTATTTT
1 ATTATTTT
1922324 ATT-TTTT
1 ATTATTTT
*
1922331 ATTACTTT
1 ATTATTTT
1922339 A
1 A
1922340 CTCGTATAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
7 14 0.30
8 19 0.40
9 8 0.17
10 6 0.13
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (8 bp):
ATTATTTT
Found at i:1934397 original size:32 final size:33
Alignment explanation
Indices: 1934356--1934417 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1934346 GCCAAACTTG
**
1934356 TATCGATACACAAAGTA-TGTATCGATACAATA
1 TATCGATACACAAAAAATTGTATCGATACAATA
1934388 TATCGATACACAAAAAATTGTATCGATACA
1 TATCGATACACAAAAAATTGTATCGATACA
1934418 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (33 bp):
TATCGATACACAAAAAATTGTATCGATACAATA
Found at i:1936649 original size:21 final size:21
Alignment explanation
Indices: 1936616--1936665 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1936606 TTGCAAGTTG
*
1936616 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1936638 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1936659 AAATAAA
1 AAATAAA
1936666 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1938483 original size:15 final size:15
Alignment explanation
Indices: 1938463--1938493 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1938453 TAAAAATATC
*
1938463 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1938478 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1938493 C
1 C
1938494 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1940587 original size:13 final size:13
Alignment explanation
Indices: 1940569--1940593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1940559 CATTTTTCTT
1940569 TGTATCGATACAC
1 TGTATCGATACAC
1940582 TGTATCGATACA
1 TGTATCGATACA
1940594 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1940748 original size:20 final size:20
Alignment explanation
Indices: 1940710--1940749 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1940700 TTTTGAAAAA
1940710 TACTTGTTTTTCACTTCAAAT
1 TACTTGTTTTTCAC-TCAAAT
1940731 TACTTCGTTTTTCA-TCAAA
1 TACTT-GTTTTTCACTCAAA
1940750 ACCAGCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTGTTTTTCACTCAAAT
Found at i:1942384 original size:19 final size:19
Alignment explanation
Indices: 1942360--1942403 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1942350 AGAGAAAATA
1942360 GATATGCAA-ATAAATTTTT
1 GATATG-AATATAAATTTTT
1942379 GATATGAATTATAAATTTTT
1 GATATGAA-TATAAATTTTT
1942399 GATAT
1 GATAT
1942404 AAATTACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 15 0.65
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
GATATGAATATAAATTTTT
Found at i:1942394 original size:20 final size:20
Alignment explanation
Indices: 1942369--1942409 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1942359 AGATATGCAA
*
1942369 ATAAATTTTTGATATGAATT
1 ATAAATTTTTGATATAAATT
1942389 ATAAATTTTTGATATAAATT
1 ATAAATTTTTGATATAAATT
1942409 A
1 A
1942410 CTTGATTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATAAATTTTTGATATAAATT
Found at i:1943171 original size:32 final size:33
Alignment explanation
Indices: 1943130--1943191 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1943120 GCCAAACTTG
**
1943130 TATCGATACACAAAGTA-TGTATCGATACAATA
1 TATCGATACACAAAAAATTGTATCGATACAATA
1943162 TATCGATACACAAAAAATTGTATCGATACA
1 TATCGATACACAAAAAATTGTATCGATACA
1943192 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (33 bp):
TATCGATACACAAAAAATTGTATCGATACAATA
Found at i:1946169 original size:78 final size:75
Alignment explanation
Indices: 1946087--1946305 Score: 219
Period size: 78 Copynumber: 2.8 Consensus size: 75
1946077 GGAATTGATG
*
1946087 GGGTTGAAGTATCCCTAAGATGAAAAATTTAACATTTTGGAAATAAAAACGGGGTTGAGTATCCC
1 GGGTTG-AGTATCCC-AAGATGAAAAATTTAATATTTTGGAAATAAAAAC-GGGTTGAGTATCCC
1946152 CTTGAAAATAAAA
63 CTTGAAAATAAAA
* * * * * * *
1946165 GGGTTGGAGTATCCCGAGATGAAAATTTTAATATTTTAGAGATAAAAGCAGGGTTGGAGTGTCTC
1 GGGTT-GAGTATCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAAC-GGGTT-GAGTATCCC
**
1946230 CTTGAAAATAATG
63 CTTGAAAATAAAA
*
1946243 GGGTTTGAGTATCCTCGCA-ATGAAAAA-TTAATATTTTTGGAAATAAAATA-GGGTTGAGTATC
1 GGG-TTGAGTATCC-C-AAGATGAAAAATTTAATA-TTTTGGAAATAAAA-ACGGGTTGAGTATC
1946305 C
61 C
1946306 TTTCAGAATT
Statistics
Matches: 116, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
77 39 0.34
78 53 0.46
79 23 0.20
80 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (75 bp):
GGGTTGAGTATCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAACGGGTTGAGTATCCCCTT
GAAAATAAAA
Found at i:1946210 original size:77 final size:75
Alignment explanation
Indices: 1946087--1946379 Score: 238
Period size: 77 Copynumber: 3.8 Consensus size: 75
1946077 GGAATTGATG
* * *
1946087 GGGTTGAAGTATCCCTAAGATGAAAAATTTAACATTTTGGAAATAAAAACGGGGTTGAGTATCCC
1 GGGTTGGAGTATCCC-GAGATG-AAAATTTAATATTTTGGAAATAAAAAC-GGGTTGAGTATCCC
1946152 CTTGAAAATAAAA
63 CTTGAAAATAAAA
* * * * *
1946165 GGGTTGGAGTATCCCGAGATGAAAATTTTAATATTTTAGAGATAAAAGCAGGGTTGGAGTGTCTC
1 GGGTTGGAGTATCCCGAGATGAAAA-TTTAATATTTTGGAAATAAAAAC-GGGTT-GAGTATCCC
**
1946230 CTTGAAAATAATG
63 CTTGAAAATAAAA
* *
1946243 GGGTTTGAGTATCCTCGCA-ATGAAAAATTAATATTTTTGGAAATAAAATA-GGGTTGAGTAT-C
1 GGGTTGGAGTATCC-CG-AGATGAAAATTTAATA-TTTTGGAAATAAAA-ACGGGTTGAGTATCC
* * * * **
1946305 CTTTCAGAATTGATG
62 CCTTGA-AAATAAAA
* *
1946320 GGGTTGGAGTATCCTCGAGA--AAAATTTATTATCTTGGAAAT-AAAACGAGGTTGGAGTATC
1 GGGTTGGAGTATCC-CGAGATGAAAATTTAATATTTTGGAAATAAAAACG-GGTT-GAGTATC
1946380 TCCTCATAAT
Statistics
Matches: 177, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
72 1 0.01
73 4 0.02
74 13 0.07
75 15 0.08
76 9 0.05
77 57 0.32
78 56 0.32
79 21 0.12
80 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (75 bp):
GGGTTGGAGTATCCCGAGATGAAAATTTAATATTTTGGAAATAAAAACGGGTTGAGTATCCCCTT
GAAAATAAAA
Found at i:1946400 original size:28 final size:28
Alignment explanation
Indices: 1946368--1946437 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
1946358 AATAAAACGA
* *
1946368 GGTTGGAGTATCTCCTCATAATTGATGG
1 GGTTGGAGTATCCCCTCAGAATTGATGG
*
1946396 GGTTGGAGTATCCCCTCGGAATTGATGG
1 GGTTGGAGTATCCCCTCAGAATTGATGG
*
1946424 GGTTGGAATATCCC
1 GGTTGGAGTATCCC
1946438 TGAGGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.31
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCAGAATTGATGG
Found at i:1946420 original size:103 final size:103
Alignment explanation
Indices: 1946293--1946514 Score: 288
Period size: 103 Copynumber: 2.2 Consensus size: 103
1946283 AAATAAAATA
** * * *
1946293 GGGTT-GAGTATCCTTTCAGAATTGATGGGGTTGGAGTAT-CCTCGAGAAAAATTTATTATCTTG
1 GGGTTGGAGTATCCCCTCAGAATTGATGGGGTTGGAATATCCCT-GAGAAAAATTTAATATCTTA
*
1946356 GAAAT-AAAACGAGGTTGGAGTATCTCCTCATAATTGATG
65 GAAATAAAAACGAGGTTGGAGTATCT-CTCAGAATTGATG
* * *
1946395 GGGTTGGAGTATCCCCTCGGAATTGATGGGGTTGGAATATCCCTGAGGAAAATTTAATATTTTAG
1 GGGTTGGAGTATCCCCTCAGAATTGATGGGGTTGGAATATCCCTGAGAAAAATTTAATATCTTAG
* * *
1946460 AAATAAAAATGGGGTTGGAGTATCTCTCGGAATTGATG
66 AAATAAAAACGAGGTTGGAGTATCTCTCAGAATTGATG
*
1946498 GGGTTGAAGTATCCCCT
1 GGGTTGGAGTATCCCCT
1946515 AAGATGAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
102 5 0.05
103 78 0.75
104 21 0.20
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.32
Consensus pattern (103 bp):
GGGTTGGAGTATCCCCTCAGAATTGATGGGGTTGGAATATCCCTGAGAAAAATTTAATATCTTAG
AAATAAAAACGAGGTTGGAGTATCTCTCAGAATTGATG
Done.