Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
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: 15949
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1057 original size:3 final size:3
Alignment explanation
Indices: 1049--1089 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1039 GTATATACAT
* *
1049 ATA ATA ATA AT- ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1090 TATGAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1061 original size:23 final size:23
Alignment explanation
Indices: 1023--1083 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1013 AAAATACTAA
1023 ACATA-AATACAT-ATATGTAT-AT
1 ACATATAATA-ATAATATG-ATGAT
1045 ACATATAATAATAATATGATGAT
1 ACATATAATAATAATATGATGAT
1068 A-ATAATAATAATAATA
1 ACAT-ATAATAATAATA
1084 ATAATATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.31
23 24 0.69
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (23 bp):
ACATATAATAATAATATGATGAT
Found at i:2269 original size:17 final size:17
Alignment explanation
Indices: 2247--2280 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2237 GACGGGTTAT
2247 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
2264 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
2281 GGCCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (17 bp):
TGGGTTGTTTGGTTTAG
Found at i:3036 original size:71 final size:72
Alignment explanation
Indices: 2939--3089 Score: 193
Period size: 71 Copynumber: 2.1 Consensus size: 72
2929 TGAAACTTAA
** * * *
2939 TTTGAAAAGCAGATTTTGAAAATACCTCAAT-G-AGTCTTGAGGCTCAACTCA-TTCTCGCAATA
1 TTTGAAAAGCAGAAATTGAAAATACCTC-ATCGTA-TCCTGAGGCTCAACTCACCTCTAGCAATA
3001 TGAGTTGAAT
64 TGAGTTG-AT
*
3011 TTTGAAAA-CAGAAATTGAAATTACCTCATCGTATCCTGAGGCTCAACTCACCTCTAGCAATATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCATCGTATCCTGAGGCTCAACTCACCTCTAGCAATATG
3075 AGTTGAT
66 AGTTGAT
3082 TTTGAAAA
1 TTTGAAAA
3090 AGTAGAATTA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
70 2 0.03
71 43 0.61
72 25 0.36
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (72 bp):
TTTGAAAAGCAGAAATTGAAAATACCTCATCGTATCCTGAGGCTCAACTCACCTCTAGCAATATG
AGTTGAT
Found at i:3508 original size:127 final size:127
Alignment explanation
Indices: 2991--3509 Score: 771
Period size: 127 Copynumber: 4.1 Consensus size: 127
2981 CTCAACTCAT
2991 TCTCGCAATATGAGTTGAATT-TTGA-AAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCT
1 TCTCGCAATATGAGTTG-ATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCT
3054 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAG-AATTAAAAGGTTCAA-CCACC
65 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACC
* *
3115 TCTGCGCTAATATAAGTTTGATTCTTGACAGACAGAAATTGAAATTACCTCATCGT-TCCTGAGG
1 TCT-CGC-AATATGAG-TTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGG
3179 CTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAAATTAAAAGGTTCAACCCAC
63 CTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTA-GAAATTAAAAGGTTCAACCCAC
3244 C
127 C
*
3245 TCTCGC-ATATAAGTTGATTCTTGACAAACAGAAATTGAAATTA-CTCATCGTAATCCTGAGGCT
1 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGT-ATCCTGAGGCT
*
3308 CAACTCA-CTCTAGCAATAT--GTTGATTTTG-AAAAGTAGGAATTAAAAGGTTCAACCCACC
65 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACC
3367 TTCTCGCAATATGAGTTGATTCTTGAACAAACAGAAATTGAAATTACCTTCATCGTATCCTGAGG
1 -TCTCGCAATATGAGTTGATTCTTG-ACAAACAGAAATTGAAATTACC-TCATCGTATCCTGAGG
* * *
3432 CTCAACTGCACCTCTAGCAATATGAGTTGATTTTGAAAAA-CA-AAAATAAAAGGCTT-AACTCA
63 CTCAACT-CACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAAAGG-TTCAACCCA
3494 CC
126 CC
3496 -CTCGCAATATGAGT
1 TCTCGCAATATGAGT
3510 CAATTTAAAA
Statistics
Matches: 365, Mismatches: 9, Indels: 39
0.88 0.02 0.09
Matches are distributed among these distances:
122 22 0.06
123 13 0.04
124 29 0.08
125 31 0.08
126 68 0.19
127 104 0.28
128 39 0.11
129 34 0.09
130 21 0.06
131 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (127 bp):
TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACC
Found at i:14081 original size:23 final size:23
Alignment explanation
Indices: 14051--14094 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
14041 AATGCTATGC
14051 ACAAATAGATATATACATATATA
1 ACAAATAGATATATACATATATA
14074 ACAAATAGATATATACATATA
1 ACAAATAGATATATACATATA
14095 ACAATGACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.30
Consensus pattern (23 bp):
ACAAATAGATATATACATATATA
Found at i:14381 original size:3 final size:3
Alignment explanation
Indices: 14356--14401 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
14346 GTATATACAT
* * *
14356 ATA ATA TATA ATG ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14402 TGAAAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:15605 original size:17 final size:17
Alignment explanation
Indices: 15583--15616 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15573 GACGGGTTAT
*
15583 TGGGTTGTTTGGTTTAG
1 TGGGTTGCTTGGTTTAG
15600 TGGGTTGCTTGGTTTAG
1 TGGGTTGCTTGGTTTAG
15617 GGCCCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.03, G:0.41, T:0.50
Consensus pattern (17 bp):
TGGGTTGCTTGGTTTAG
Done.