Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold953
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: 66181
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:19286 original size:42 final size:44
Alignment explanation
Indices: 19199--19291 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 44
19189 ATAAATAAAG
* * ** *
19199 ATATATATATATGAATTACAAAACATGAAAATATAAGTATTTAC
1 ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
* *
19243 ATATATAAATA-GATTTAAAAAATAT-AAAATATAAACATGTAC
1 ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
19285 AT-TATAA
1 ATATATAA
19292 GAACGTAGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.12
42 16 0.38
43 11 0.26
44 10 0.24
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (44 bp):
ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
Found at i:19609 original size:34 final size:34
Alignment explanation
Indices: 19544--19609 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
19534 TTTAATAATA
* ** *
19544 TTAATAATAATGCTAAATAATAATTATAATAGTT
1 TTAATAATAATGATAAATAATAAAAAAAATAGTT
19578 TTAATAATAAT-ATATAATAATAAAAAAAATAG
1 TTAATAATAATGATA-AATAATAAAAAAAATAG
19610 CACATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (34 bp):
TTAATAATAATGATAAATAATAAAAAAAATAGTT
Found at i:20775 original size:16 final size:17
Alignment explanation
Indices: 20756--20789 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20746 ATTAATGTTT
20756 TGGGCTA-TTTGGGCTG
1 TGGGCTAGTTTGGGCTG
*
20772 TGGGTTAGTTTGGGCTG
1 TGGGCTAGTTTGGGCTG
20789 T
1 T
20790 TAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.44, T:0.41
Consensus pattern (17 bp):
TGGGCTAGTTTGGGCTG
Found at i:25954 original size:18 final size:18
Alignment explanation
Indices: 25912--25954 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
25902 AATTTAAAAA
25912 AAAAATTTGTAATTTTTT
1 AAAAATTTGTAATTTTTT
*** *
25930 TTGAATTTTTAATTTTTT
1 AAAAATTTGTAATTTTTT
25948 AAAAATT
1 AAAAATT
25955 AATTCAATGT
Statistics
Matches: 18, Mismatches: 7, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
AAAAATTTGTAATTTTTT
Found at i:26943 original size:184 final size:184
Alignment explanation
Indices: 26624--26969 Score: 647
Period size: 184 Copynumber: 1.9 Consensus size: 184
26614 TATATATATA
* *
26624 TGTGTGCGCGCCATATAATATTTATTGTATTAATTTTGGTGAATCGATTAATTAATTACTTTTGA
1 TGTGCGCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATCGATTAATTAATTACTTTTGA
* *
26689 ACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTTAATGACCGATCGA
66 ACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAA
26754 TTTACTAAATTAATTTGATTTTAACCACACATCATATATATATGTGTGTGTGTG
131 TTTACTAAATTAATTTGATTTTAACCACACATCATATATATATGTGTGTGTGTG
*
26808 TGTGCGCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATTGATTAATTAATTACTTTTGA
1 TGTGCGCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATCGATTAATTAATTACTTTTGA
26873 ACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAA
66 ACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAA
26938 TTTACTAAATTAATTTGATTTTAACCACACAT
131 TTTACTAAATTAATTTGATTTTAACCACACAT
26970 AAATTATATT
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 157 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (184 bp):
TGTGCGCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATCGATTAATTAATTACTTTTGA
ACTGAATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAA
TTTACTAAATTAATTTGATTTTAACCACACATCATATATATATGTGTGTGTGTG
Found at i:28806 original size:33 final size:34
Alignment explanation
Indices: 28739--28807 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
28729 AATAAAATTT
*
28739 AAATATTTTTAAATTACATTAATAATAAATAATA
1 AAATATATTTAAATTACATTAATAATAAATAATA
* * *
28773 AAATATATTTAAATTA-TTTTATATTAAATAATA
1 AAATATATTTAAATTACATTAATAATAAATAATA
28806 AA
1 AA
28808 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 16 0.52
34 15 0.48
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
AAATATATTTAAATTACATTAATAATAAATAATA
Found at i:52067 original size:22 final size:23
Alignment explanation
Indices: 51968--52117 Score: 101
Period size: 24 Copynumber: 6.3 Consensus size: 23
51958 GGACTCACCG
*
51968 CAGCTCGTATGAGCTTACCGATATTT
1 CAGCTCGTATGAGCTTA-C--TGTTT
* * * *
51994 TAGTTCGTAAGAGCTTACTATTTT
1 CAGCTCGTATGAGCTTACT-GTTT
* * *
52018 CAGTTCAT-TGGAGCTTAATGTTT
1 CAGCTCGTAT-GAGCTTACTGTTT
52041 CAGCTCGTATGAGCTTACTG-TT
1 CAGCTCGTATGAGCTTACTGTTT
52063 CAGCTCGGTA-GAGCTTACTGTTTT
1 CAGCTC-GTATGAGCTTACTG-TTT
*
52087 CAGCTC-AATAGAGCTTACTGTTCAT
1 CAGCTCGTAT-GAGCTTACTGTT--T
52112 CAGCTC
1 CAGCTC
52118 AAGAGGAGCT
Statistics
Matches: 101, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
22 19 0.19
23 24 0.24
24 36 0.36
25 8 0.08
26 14 0.14
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (23 bp):
CAGCTCGTATGAGCTTACTGTTT
Found at i:52098 original size:24 final size:24
Alignment explanation
Indices: 52003--52130 Score: 111
Period size: 24 Copynumber: 5.4 Consensus size: 24
51993 TTAGTTCGTA
* * *
52003 AGAGCTTACTATTTTCAGTTCATT
1 AGAGCTTACTGTTTTCAGCTCAAT
* * *
52027 GGAGCTTAATG-TTTCAGCTC-GT
1 AGAGCTTACTGTTTTCAGCTCAAT
**
52049 ATGAGCTTACTG--TTCAGCTCGGT
1 A-GAGCTTACTGTTTTCAGCTCAAT
52072 AGAGCTTACTGTTTTCAGCTCAAT
1 AGAGCTTACTGTTTTCAGCTCAAT
* *
52096 AGAGCTTACTGTTCATCAGCTCAAG
1 AGAGCTTACTGTT-TTCAGCTCAAT
52121 AGGAGCTTAC
1 A-GAGCTTAC
52131 CGATCATGGC
Statistics
Matches: 87, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
22 19 0.22
23 20 0.23
24 30 0.34
25 10 0.11
26 8 0.09
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (24 bp):
AGAGCTTACTGTTTTCAGCTCAAT
Found at i:52137 original size:26 final size:25
Alignment explanation
Indices: 52086--52137 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
52076 CTTACTGTTT
* * *
52086 TCAGCTCAATAGAGCTTACTGTTCA
1 TCAGCTCAAGAGAGCTTACCGATCA
52111 TCAGCTCAAGAGGAGCTTACCGATCA
1 TCAGCTCAAGA-GAGCTTACCGATCA
52137 T
1 T
52138 GGCTCGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACCGATCA
Found at i:52255 original size:20 final size:20
Alignment explanation
Indices: 52230--52281 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
52220 CAGCGGGCAC
*
52230 AATTACTGTTTATACAGATG
1 AATTACTGTTTATACAAATG
*
52250 AATTACAG-TT-TACAAATG
1 AATTACTGTTTATACAAATG
*
52268 AATTATTGTTTATA
1 AATTACTGTTTATA
52282 TGATATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 13 0.50
19 4 0.15
20 9 0.35
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (20 bp):
AATTACTGTTTATACAAATG
Found at i:59097 original size:55 final size:54
Alignment explanation
Indices: 58989--59135 Score: 172
Period size: 55 Copynumber: 2.7 Consensus size: 54
58979 ATTAGGGTTT
* *
58989 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC-
1 AAGGA-ACCATGTAAGACCATGCCAAGGCATGGC-ATTGATAAGGTTTATAAGGCA
* * *
59044 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAA-GTTACTATAAGGCA
1 AAGG-AACCATGTAAGACCATGCCAAGGCATGGCATTGATAAGGTT--TATAAGGCA
**
59100 AAGGTCCCATGTAAGACCATGCCAAGGCATGGCATT
1 AAGGAACCATGTAAGACCATGCCAAGGCATGGCATT
59136 AAGACCATGC
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
53 3 0.04
54 7 0.09
55 63 0.81
56 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGAACCATGTAAGACCATGCCAAGGCATGGCATTGATAAGGTTTATAAGGCA
Found at i:59138 original size:24 final size:24
Alignment explanation
Indices: 59111--59159 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
59101 AGGTCCCATG
*
59111 TAAGACCATGCCAAGGCATGGCAT
1 TAAGACCATGCCAAGACATGGCAT
59135 TAAGACCATGCCAAGACATGGCAT
1 TAAGACCATGCCAAGACATGGCAT
59159 T
1 T
59160 GGTGAGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (24 bp):
TAAGACCATGCCAAGACATGGCAT
Found at i:59451 original size:16 final size:16
Alignment explanation
Indices: 59430--59460 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59420 ATAAATTTGA
59430 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
59446 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
59461 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:62101 original size:27 final size:27
Alignment explanation
Indices: 62071--62248 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
62061 ATATTGAGTC
* * * *
62071 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
62098 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
62125 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
62153 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
62180 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
62207 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
62234 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
62249 GTCCAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:62210 original size:82 final size:81
Alignment explanation
Indices: 62092--62247 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
62082 TGCTATATAA
* *
62092 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
62157 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
62174 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
62238 CACTTAGTGC
65 CACTTAGTGC
62248 TGTCCAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:63809 original size:21 final size:20
Alignment explanation
Indices: 63776--63815 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
63766 TTCATCCTTT
* *
63776 TTTTCTTTTTAATTCACTTC
1 TTTTATTTTTAATCCACTTC
63796 TTTTATTTTCTAATCCACTT
1 TTTTATTTT-TAATCCACTT
63816 ACCAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATTTTTAATCCACTTC
Done.