Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1611
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: 240859
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:221976 original size:16 final size:17
Alignment explanation
Indices: 221955--221986 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
221945 AGTTTACATG
221955 TTGTATTTA-CAAATAA
1 TTGTATTTATCAAATAA
221971 TTGTATTTATCAAATA
1 TTGTATTTATCAAATA
221987 TGAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
TTGTATTTATCAAATAA
Found at i:227145 original size:44 final size:46
Alignment explanation
Indices: 227055--227146 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 46
227045 GGCTATAGTG
* * *
227055 GAATAGAGTTGTAATAAGTAATTCAATTGTTTGGTTGAATGTAATA
1 GAATAGAATTGTAATAAGTAATTCAATTGTTTGGTTAAATGGAATA
*
227101 GAATAGAATTGTAAT-AGT-ATT-ATTGTGTTTGGTTAAATGGAATA
1 GAATAGAATTGTAATAAGTAATTCAAT-TGTTTGGTTAAATGGAATA
227145 GA
1 GA
227147 TATGTAATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 22 0.54
45 3 0.07
46 14 0.34
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.39
Consensus pattern (46 bp):
GAATAGAATTGTAATAAGTAATTCAATTGTTTGGTTAAATGGAATA
Found at i:227316 original size:33 final size:33
Alignment explanation
Indices: 227278--227342 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
227268 CTTAATATAA
227278 TTATTTTTATAT-TAAATTATATTAAAAGATTTT
1 TTATTTTTATATGT-AATTATATTAAAAGATTTT
*
227311 TTATTTTTATATGTAATTATATTAAAATATTT
1 TTATTTTTATATGTAATTATATTAAAAGATTT
227343 AAAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (33 bp):
TTATTTTTATATGTAATTATATTAAAAGATTTT
Found at i:228667 original size:4 final size:4
Alignment explanation
Indices: 228651--229502 Score: 856
Period size: 4 Copynumber: 219.5 Consensus size: 4
228641 TCATATCTAA
* *
228651 ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACCT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
228699 ACCT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
228747 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * ** *
228793 ACAT GCAT GCAT ACAT GCAT --AT ACAT GCAT ACAT GTAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* ** *
228839 ACAT ACAT GCAT --AT ACAT GTAT ACAT ACAT ACAT ACAT GCAT --AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
228883 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT --AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
** * * *
228929 GTAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT TCAT ACAT ACAT ATAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
** * * *
228977 GTAT ACAT ACAT ACAT ACAT --AT ACAT CCAT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
229023 ACAT ACAT ACAT --AT ACAT GCAT ACAT GCAT --AT ACAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
229067 GCAT ACAT GCAT ACAT GCAT ACAT ACAT ACAT --AT ACAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
229113 GCAT --AT ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* **
229159 ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT GTAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
229205 ACAT ACAT GCAT AC-- ACAT ACAT ACAT GCAT GCAT GCAT GCAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
229251 GCAT ACAT CCAT ACAT GCAT ACAT ACAT ACAT ACAT GCAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * *
229299 CCAT GCAT GCAT ACAT CCAT GCAT GCAT --AT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * *
229345 ACAT ACAT CCAT GCAT GCAT ACAT CCAT ATAT GCAT ACAT GCAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
229393 GCAT ACAT GCAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
229441 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
229489 ACAT GCAT ACAT AC
1 ACAT ACAT ACAT AC
229503 CTGTCCTCCA
Statistics
Matches: 712, Mismatches: 110, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
2 26 0.04
4 686 0.96
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:230905 original size:12 final size:12
Alignment explanation
Indices: 230884--230917 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
230874 AATTAACATG
*
230884 ATGAATATTAGC
1 ATGAACATTAGC
230896 ATGAACATTAGC
1 ATGAACATTAGC
230908 ATGAACATTA
1 ATGAACATTA
230918 TCAAAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (12 bp):
ATGAACATTAGC
Found at i:235380 original size:93 final size:92
Alignment explanation
Indices: 235268--235437 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 92
235258 GCCCCTAAGT
*
235268 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTC-GACTCAACTCA
235332 ACGAGTTAGGATGCCTAGTTACATTTCAC
64 ACGAGTTAGGATGCCTAGTTACATTTCAC
* *
235361 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGACTCAACTCAAC
*
235426 GAGTTCGGATGC
66 GAGTTAGGATGC
235438 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 26 0.36
93 46 0.64
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGACTCAACTCAAC
GAGTTAGGATGCCTAGTTACATTTCAC
Found at i:235453 original size:45 final size:45
Alignment explanation
Indices: 235263--235434 Score: 129
Period size: 46 Copynumber: 3.8 Consensus size: 45
235253 AACCCGCCCC
* ** *
235263 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGT-TCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGAATCT-GCAACCA
* * **
235309 TAAGTGAACTCAGACTCAACTCAACGAGTTAGG-ATGCCTAGTTA-CA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAAT--CT-GCAACCA
* * * *
235355 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-ATCTGCAACCA
235402 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
235435 TGCTCAACCA
Statistics
Matches: 99, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
44 1 0.01
45 26 0.26
46 37 0.37
47 31 0.31
48 2 0.02
49 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATCTGCAACCA
Done.