Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2544
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: 34964
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4248 original size:4 final size:4
Alignment explanation
Indices: 4239--4265 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4229 AAACTAAGTA
4239 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
4266 AATAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:14005 original size:29 final size:31
Alignment explanation
Indices: 13943--14007 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
13933 AGCAAAAATT
*
13943 AATTGAGCTGAATTTGTAAGTATTTGAGCTA
1 AATTGAGCTGAATTTGTAACTATTTGAGCTA
13974 AATTGAGCTG-ATTTG-AACTCA-TTGAGCTA
1 AATTGAGCTGAATTTGTAACT-ATTTGAGCTA
14003 AATTG
1 AATTG
14008 GAAGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.50
30 6 0.19
31 10 0.31
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (31 bp):
AATTGAGCTGAATTTGTAACTATTTGAGCTA
Found at i:15337 original size:65 final size:64
Alignment explanation
Indices: 15266--15401 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 64
15256 AGTGTTGTTC
* * * *
15266 TTAATTAATCTAGTTCCTAGGATTATTTATTG-ATGCATGAGTTAAGTTCATTTAATTATGCTTC
1 TTAATTAAACTAGTT-CTAGGAATAATTATTGCATACATG-GTTAAGTTCATTTAATTATGCTTC
15330 T
64 T
* * * * *
15331 TTAATTAAACTAGTTGTTGGAATAATTATTGCATATATGTTTTAGTTCATTTAATTATGCTTCT
1 TTAATTAAACTAGTTCTAGGAATAATTATTGCATACATGGTTAAGTTCATTTAATTATGCTTCT
15395 TTAATTA
1 TTAATTA
15402 TTCTTCTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 42 0.69
65 19 0.31
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (64 bp):
TTAATTAAACTAGTTCTAGGAATAATTATTGCATACATGGTTAAGTTCATTTAATTATGCTTCT
Found at i:15399 original size:14 final size:14
Alignment explanation
Indices: 15380--15415 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
15370 TTTTAGTTCA
15380 TTTAATTATGCTTC
1 TTTAATTATGCTTC
*
15394 TTTAATTATTCTTC
1 TTTAATTATGCTTC
15408 TTTAATTA
1 TTTAATTA
15416 AACAGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTATGCTTC
Found at i:15924 original size:19 final size:18
Alignment explanation
Indices: 15888--15927 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15878 TTTCCACTCG
*
15888 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
15906 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
15925 TTT
1 TTT
15928 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:16999 original size:12 final size:13
Alignment explanation
Indices: 16981--17015 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
16971 AACTAGCTCT
*
16981 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAA
16995 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
17008 TTTTTTTT
1 TTTTTTTT
17016 TTCACAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:16999 original size:14 final size:15
Alignment explanation
Indices: 16980--17022 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
16970 AAACTAGCTC
16980 TTTTTTTTTCACAA-
1 TTTTTTTTTCACAAT
*
16994 TTTTTTTTTCAAAAT
1 TTTTTTTTTCACAAT
17009 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
17023 CTTGATATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTTTTTCACAAT
Found at i:17080 original size:9 final size:10
Alignment explanation
Indices: 17065--17114 Score: 64
Period size: 10 Copynumber: 4.7 Consensus size: 10
17055 ACCAAAATTT
17065 TTTTTTTGAA
1 TTTTTTTGAA
17075 TTTTTTTTTGAA
1 --TTTTTTTGAA
17087 TTTTTTTGAA
1 TTTTTTTGAA
*
17097 TTTTTTTTGAG
1 -TTTTTTTGAA
17108 TTTTTTT
1 TTTTTTT
17115 TCGAGAAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 17 0.47
11 9 0.25
12 10 0.28
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:17080 original size:11 final size:11
Alignment explanation
Indices: 17064--17115 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
17054 AACCAAAATT
17064 TTTTTTTTGAA
1 TTTTTTTTGAA
17075 TTTTTTTTTGAA
1 -TTTTTTTTGAA
17087 -TTTTTTTGAA
1 TTTTTTTTGAA
*
17097 TTTTTTTTGAG
1 TTTTTTTTGAA
17108 TTTTTTTT
1 TTTTTTTT
17116 CGAGAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
10 10 0.26
11 17 0.45
12 11 0.29
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:17080 original size:12 final size:12
Alignment explanation
Indices: 17063--17115 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
17053 AAACCAAAAT
17063 TTTTTTTTTGAA
1 TTTTTTTTTGAA
17075 TTTTTTTTTGAA
1 TTTTTTTTTGAA
17087 --TTTTTTTGAA
1 TTTTTTTTTGAA
*
17097 -TTTTTTTTGAG
1 TTTTTTTTTGAA
17108 TTTTTTTT
1 TTTTTTTT
17116 CGAGAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
10 10 0.26
11 9 0.24
12 19 0.50
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:17093 original size:22 final size:21
Alignment explanation
Indices: 17065--17114 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
17055 ACCAAAATTT
17065 TTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTGAA-TTTTTTTTGAA
*
17087 TTTTTTTGAATTTTTTTTGAG
1 TTTTTTTGAATTTTTTTTGAA
17108 TTTTTTT
1 TTTTTTT
17115 TCGAGAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (21 bp):
TTTTTTTGAATTTTTTTTGAA
Found at i:19026 original size:16 final size:16
Alignment explanation
Indices: 19005--19036 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18995 TAATGTGTTT
19005 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
19021 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
19037 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:19360 original size:72 final size:73
Alignment explanation
Indices: 19223--19370 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 73
19213 GCAGGTACAT
* * * *
19223 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGCGCAT
*
19288 GGGACTTG
66 GGGACGTG
* * * * * *
19296 GGACGGCATTTAAAGCTAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGCGCA
1 GGACGGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGCGCA
19359 TGGGACGTG
65 TGGGACGTG
19368 GGA
1 GGA
19371 TAGCATTAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
72 36 0.57
73 24 0.38
74 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGCGCAT
GGGACGTG
Found at i:22465 original size:14 final size:14
Alignment explanation
Indices: 22446--22472 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22436 CATGAAAATA
22446 AAAAACCTCACAAC
1 AAAAACCTCACAAC
22460 AAAAACCTCACAA
1 AAAAACCTCACAA
22473 ATCTATCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.33, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAACCTCACAAC
Found at i:23499 original size:22 final size:23
Alignment explanation
Indices: 23474--23522 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
23464 ATCAGCTTCT
23474 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
23496 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
23518 TTAAT
1 TTAAT
23523 CATACGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:31226 original size:13 final size:13
Alignment explanation
Indices: 31194--31227 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
31184 TTGTAGATTC
31194 AAAAAAA-TTGAA
1 AAAAAAATTTGAA
31206 AAAAAAATTTGAA
1 AAAAAAATTTGAA
31219 AAAAAAATT
1 AAAAAAATT
31228 GCATACGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:33118 original size:17 final size:18
Alignment explanation
Indices: 33096--33135 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
33086 CATTTCTTTT
33096 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
*
33113 TCTTTT-TATCACTCATC
1 TCTTTTGAATCACTCATC
33130 T-TTTTG
1 TCTTTTG
33136 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.15, C:0.25, G:0.05, T:0.55
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Done.