Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold473
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: 67086
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:10675 original size:13 final size:13
Alignment explanation
Indices: 10657--10681 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10647 GCCGGATCAC
10657 AGATTTCAAGAAG
1 AGATTTCAAGAAG
10670 AGATTTCAAGAA
1 AGATTTCAAGAA
10682 TCAAGAAAAT
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:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (13 bp):
AGATTTCAAGAAG
Found at i:16883 original size:18 final size:19
Alignment explanation
Indices: 16860--16898 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
16850 TTTATCTCAA
*
16860 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
16878 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
16897 TT
1 TT
16899 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:16937 original size:18 final size:18
Alignment explanation
Indices: 16916--16965 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
16906 AAACTTTTTT
16916 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
16934 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
16952 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
16966 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:17024 original size:42 final size:42
Alignment explanation
Indices: 16969--17065 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
16959 CTTTTTCTTT
* * *
16969 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
17010 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
17052 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
17066 CTCATAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:17043 original size:21 final size:21
Alignment explanation
Indices: 16976--17043 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
16966 TTTTTCTTTC
*
16976 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
16997 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
17017 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
17039 ATTTC
1 ATTTC
17044 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:19470 original size:10 final size:10
Alignment explanation
Indices: 19457--19491 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
19447 AAGCTCGGTT
19457 GAGCTCAAAC
1 GAGCTCAAAC
*
19467 GAGCTGAAAC
1 GAGCTCAAAC
*
19477 GAGCTCAAAT
1 GAGCTCAAAC
19487 GAGCT
1 GAGCT
19492 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:19500 original size:20 final size:20
Alignment explanation
Indices: 19454--19501 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
19444 AGTAAGCTCG
19454 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
19474 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
19494 GTTGAGCT
1 GTTGAGCT
19502 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:22102 original size:26 final size:26
Alignment explanation
Indices: 22071--22178 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
22061 TGAAATGCCC
*
22071 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
22097 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
22123 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
22149 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
22175 ATCA
1 ATCA
22179 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:26144 original size:15 final size:15
Alignment explanation
Indices: 26124--26171 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
26114 TCAAAGATGG
26124 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
26139 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
26153 GTTTATGGATATAAA
1 GTTTATGGATATGAA
26168 GTTT
1 GTTT
26172 TCGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:26158 original size:14 final size:14
Alignment explanation
Indices: 26118--26161 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
26108 AAGGATTCAA
26118 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
26132 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
26147 AGATGGGTTTATGG
1 AGATGGGTTTATGG
26161 A
1 A
26162 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:29068 original size:21 final size:21
Alignment explanation
Indices: 29042--29104 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
29032 TTGGTATTTG
*
29042 GGAATTGGTACAAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
29063 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
29084 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
29105 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:29805 original size:12 final size:12
Alignment explanation
Indices: 29788--29813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29778 ATCATTAAAA
29788 TCAGCTGAACAT
1 TCAGCTGAACAT
29800 TCAGCTGAACAT
1 TCAGCTGAACAT
29812 TC
1 TC
29814 CTCATGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (12 bp):
TCAGCTGAACAT
Found at i:31299 original size:23 final size:22
Alignment explanation
Indices: 31247--31299 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31237 TCCACGTCTT
*
31247 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
31269 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
31292 TTTCTTTT
1 TTTCTTTT
31300 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39422 original size:11 final size:11
Alignment explanation
Indices: 39392--39425 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
39382 GAAGAGCCAA
39392 ATGGTGTGAAC
1 ATGGTGTGAAC
*
39403 ATGG-CTGAAC
1 ATGGTGTGAAC
39413 ATGGTGTGAAC
1 ATGGTGTGAAC
39424 AT
1 AT
39426 CTTAATGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.26
Consensus pattern (11 bp):
ATGGTGTGAAC
Found at i:50690 original size:21 final size:23
Alignment explanation
Indices: 50645--50691 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
50635 TCACCTGCAA
* *
50645 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
50668 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
50689 TAA
1 TAA
50692 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:53883 original size:19 final size:18
Alignment explanation
Indices: 53847--53886 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53837 TTTCCACTCG
*
53847 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
53865 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
53884 TTT
1 TTT
53887 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:54991 original size:14 final size:14
Alignment explanation
Indices: 54941--54989 Score: 89
Period size: 14 Copynumber: 3.4 Consensus size: 14
54931 CTAGCTTCTC
54941 TTTTTTTCACAATT
1 TTTTTTTCACAATT
54955 TTTTTTTCACAATT
1 TTTTTTTCACAATT
54969 TTTTTTTCACGAATT
1 TTTTTTTCAC-AATT
54984 TTTTTT
1 TTTTTT
54990 CAACTTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.18, C:0.12, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:55065 original size:11 final size:12
Alignment explanation
Indices: 55031--55062 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
55021 GAAACCAAAT
55031 TTTTTTTTTGAA
1 TTTTTTTTTGAA
55043 TTTTTTTTTGAA
1 TTTTTTTTTGAA
55055 TTTTTTTT
1 TTTTTTTT
55063 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:59420 original size:21 final size:23
Alignment explanation
Indices: 59375--59421 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
59365 TCACCTGCAA
* *
59375 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
59398 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
59419 TAA
1 TAA
59422 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:61215 original size:22 final size:22
Alignment explanation
Indices: 61187--61230 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
61177 TTTTGAACCA
61187 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
61209 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
61231 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:64031 original size:45 final size:45
Alignment explanation
Indices: 63802--64027 Score: 370
Period size: 45 Copynumber: 5.1 Consensus size: 45
63792 TCGGCCATGG
* * * *
63802 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
63847 TGCTTCCTTAAATTCTTCCATGAATTA-GCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
63891 TGCTTCCT--AATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
63934 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
63979 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTC-AA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
64023 TGCTT
1 TGCTT
64028 TCCTTAATTT
Statistics
Matches: 172, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
42 17 0.10
43 25 0.15
44 31 0.18
45 99 0.58
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Done.