Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold616
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: 121719
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.10
Warning! 82514 characters in sequence are not A, C, G, or T
Found at i:29002 original size:15 final size:16
Alignment explanation
Indices: 28982--29011 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28972 TCAGGACGGT
28982 CTCGATTTC-TTGGAC
1 CTCGATTTCGTTGGAC
28997 CTCGATTTCGTTGGA
1 CTCGATTTCGTTGGA
29012 ACCGTTGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (16 bp):
CTCGATTTCGTTGGAC
Found at i:29722 original size:12 final size:12
Alignment explanation
Indices: 29702--29742 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
29692 TATATATATA
*
29702 TTTTCGAATTTT
1 TTTTTGAATTTT
29714 TTTTTGAATTTT
1 TTTTTGAATTTT
*
29726 TTTTTCAAATTTT
1 TTTTT-GAATTTT
29739 TTTT
1 TTTT
29743 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTGAATTTT
Found at i:29726 original size:13 final size:13
Alignment explanation
Indices: 29702--29742 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29692 TATATATATA
*
29702 TTTTCGAATTTTT
1 TTTTCAAATTTTT
*
29715 TTTT-GAATTTTT
1 TTTTCAAATTTTT
29727 TTTTCAAATTTTT
1 TTTTCAAATTTTT
29740 TTT
1 TTT
29743 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTCAAATTTTT
Found at i:35213 original size:16 final size:17
Alignment explanation
Indices: 35181--35213 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35171 TAATTTTTGG
35181 GTCAAAAAAATTCAAGA
1 GTCAAAAAAATTCAAGA
*
35198 GTCAAGAAAA-TCAAGA
1 GTCAAAAAAATTCAAGA
35214 TTCCATATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
GTCAAAAAAATTCAAGA
Found at i:68940 original size:14 final size:14
Alignment explanation
Indices: 68912--68946 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
68902 TTTTCTTTTC
68912 TTTTTTAACTCAAA
1 TTTTTTAACTCAAA
68926 TTATTTTAA-TCAAA
1 TT-TTTTAACTCAAA
68940 TTTTTTA
1 TTTTTTA
68947 TATTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTTAACTCAAA
Found at i:72061 original size:41 final size:40
Alignment explanation
Indices: 72016--72146 Score: 208
Period size: 41 Copynumber: 3.2 Consensus size: 40
72006 AATTCGGCCA
*
72016 AACATGTAGTAGTAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGGCATATTTAT
*
72057 AACATGTAGTGACAGCATTAAATTCATCCAGGCATATTTAT
1 AACATGTAGTG-CAGCATTAAATTCGTCCAGGCATATTTAT
*
72098 AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGGCATATTTAT
72139 AACATGTA
1 AACATGTA
72147 TGAAAATAGG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.01
41 82 0.98
42 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (40 bp):
AACATGTAGTGCAGCATTAAATTCGTCCAGGCATATTTAT
Found at i:72349 original size:20 final size:19
Alignment explanation
Indices: 72324--72374 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
72314 AGCTAATAAC
* *
72324 GAGCTCAATGTGCTGACTTT
1 GAGCTCAATGAGCTAAC-TT
*
72344 GAGCTCGATGAGCTAACTT
1 GAGCTCAATGAGCTAACTT
72363 GAGCTCGAATGA
1 GAGCTC-AATGA
72375 ACCAAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (19 bp):
GAGCTCAATGAGCTAACTT
Found at i:74482 original size:39 final size:33
Alignment explanation
Indices: 74440--74507 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
74430 TTGAGGCCAA
74440 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
1 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
74473 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
1 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
74506 AC
1 AC
74508 ACTGATAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (33 bp):
ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
Found at i:74861 original size:27 final size:27
Alignment explanation
Indices: 74820--75095 Score: 351
Period size: 27 Copynumber: 10.2 Consensus size: 27
74810 ACTTGATGGC
* * *
74820 TAAAATTATCAAAATACCCTCAAAAGG
1 TAAAATTACCGAAATACCCTCAAAGGG
*
74847 TAAAATTACTGAAATACCCTCGAAA-GG
1 TAAAATTACCGAAATACCCTC-AAAGGG
* * **
74874 TAAAAGTACCAAAATACCCTTGAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
*
74901 TAAAATTACCGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
*
74928 TAAAATTATCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
* *
74955 TAAAATTACTGATATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
74982 TAAAATTACCGAAATACCCAT-AAAGGG
1 TAAAATTACCGAAATACCC-TCAAAGGG
* * *
75009 TAAAATTACCAAAATACACTCGAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
75036 TAAAATTACCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
* *
75063 TAAAATTACCAAAATACCC-CTGAAGGG
1 TAAAATTACCGAAATACCCTC-AAAGGG
75090 TAAAAT
1 TAAAAT
75096 AACTGTTATA
Statistics
Matches: 218, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
26 4 0.02
27 210 0.96
28 4 0.02
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCAAAGGG
Found at i:79221 original size:25 final size:25
Alignment explanation
Indices: 79179--79229 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
79169 TTGGGTTGTG
*
79179 TGCTGACGCATGAAGGTAAGGTGAT
1 TGCTGACGCAGGAAGGTAAGGTGAT
* *
79204 TGCTGATGCAGGAGGGTAAGGTGAT
1 TGCTGACGCAGGAAGGTAAGGTGAT
79229 T
1 T
79230 CCTTATGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.25
Consensus pattern (25 bp):
TGCTGACGCAGGAAGGTAAGGTGAT
Found at i:82269 original size:197 final size:197
Alignment explanation
Indices: 81934--82292 Score: 619
Period size: 197 Copynumber: 1.8 Consensus size: 197
81924 TATTTGCAAT
81934 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
1 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
* *
81999 GAGTCACTTGTGTTTCCGATGGTAAAATTCAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
66 GAGTCACTTGTGTTCCCGATGGTAAAATTAAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
*
82064 CAGAGAAAGATAGGATTAACAAAGAAAACGTATTTTTAAAGTTCAACCCTGGGAGTGATAAATAA
131 CAGAGAAAGATAGGAATAACAAAGAAAACGTATTTTTAAAGTTCAACCCTGGGAGTGATAAATAA
82129 TA
196 TA
* * * *
82131 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCGATCTCGTATTCGATGGTTGGATC
1 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
* * *
82196 GAGTCGCTTGTGTTCCCGATGGTAAAATTAAGTAGTAAGGGTTTCGTTTAACAAAAGGCTAATTT
66 GAGTCACTTGTGTTCCCGATGGTAAAATTAAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
*
82261 CGGAGAAAGATAGGAATAACAAAGAAAACGTA
131 CAGAGAAAGATAGGAATAACAAAGAAAACGTA
82293 AAGTTGATAA
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 151 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (197 bp):
GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
GAGTCACTTGTGTTCCCGATGGTAAAATTAAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
CAGAGAAAGATAGGAATAACAAAGAAAACGTATTTTTAAAGTTCAACCCTGGGAGTGATAAATAA
TA
Found at i:106084 original size:30 final size:30
Alignment explanation
Indices: 106026--106084 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
106016 TTGAAAAGGT
* *
106026 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
106056 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
106085 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:115858 original size:20 final size:20
Alignment explanation
Indices: 115835--115881 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
115825 GGGTTGAGGT
115835 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
115855 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
115875 TGAGCTG
1 TGAGCTG
115882 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:116780 original size:14 final size:14
Alignment explanation
Indices: 116761--116794 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
116751 TGCTGATTTC
116761 TTTTTTTCACAAAT
1 TTTTTTTCACAAAT
116775 TTTTTTTCACAAAT
1 TTTTTTTCACAAAT
116789 TTTTTT
1 TTTTTT
116795 ATATTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTCACAAAT
Done.