Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1878
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, 738
Length: 1230
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Found at i:238 original size:132 final size:132
Alignment explanation
Indices: 1--268 Score: 509
Period size: 132 Copynumber: 2.0 Consensus size: 132
1 GGACTAATGGCTTAAATCTGCTTCTCCACTTTATTTGGAAGCTAAGATTCACAATCTTCGATCCG
1 GGACTAATGGCTTAAATCTGCTTCTCCACTTTATTTGGAAGCTAAGATTCACAATCTTCGATCCG
*
66 CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
66 CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCCTAGGGTGA
131 GA
131 GA
133 GGACTAATGGCTTAAATCTGCTTCTCCACTTTATTTGGAAGCTAAGATTCACAATCTTCGATCCG
1 GGACTAATGGCTTAAATCTGCTTCTCCACTTTATTTGGAAGCTAAGATTCACAATCTTCGATCCG
*
198 CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTATTGCCTAGGGTGA
66 CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCCTAGGGTGA
*
263 TA
131 GA
265 GGAC
1 GGAC
269 GCAATCTTCA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
GGACTAATGGCTTAAATCTGCTTCTCCACTTTATTTGGAAGCTAAGATTCACAATCTTCGATCCG
CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCCTAGGGTGA
GA
Found at i:247 original size:44 final size:42
Alignment explanation
Indices: 198--304 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
188 CTTCGATCCG
**
198 CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCCTAGGGTGACAGAA-C-GCAATCTTCAACCTA
* * *
242 CTCCACTATTGCCTAGGGTGATAGGACGCAATCTTCAACCTA
1 CTCCACTACTGCCTAGGGTGACAGAACGCAATCTTCAACCTA
*
284 CTCCACTATTGCCTAGGGTGA
1 CTCCACTACTGCCTAGGGTGA
305 TAGGACTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 36 0.62
43 1 0.02
44 21 0.36
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (42 bp):
CTCCACTACTGCCTAGGGTGACAGAACGCAATCTTCAACCTA
Found at i:284 original size:42 final size:42
Alignment explanation
Indices: 227--310 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
217 GACAGAATCT
227 GCAATCTTCAACCTACTCCACTATTGCCTAGGGTGATAGGAC
1 GCAATCTTCAACCTACTCCACTATTGCCTAGGGTGATAGGAC
269 GCAATCTTCAACCTACTCCACTATTGCCTAGGGTGATAGGAC
1 GCAATCTTCAACCTACTCCACTATTGCCTAGGGTGATAGGAC
311 TAATGGCTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (42 bp):
GCAATCTTCAACCTACTCCACTATTGCCTAGGGTGATAGGAC
Found at i:314 original size:174 final size:174
Alignment explanation
Indices: 66--442 Score: 549
Period size: 174 Copynumber: 2.2 Consensus size: 174
56 CTTCGATCCG
** * * *
66 CTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1 CTCCACTACTGCCTAGGGTGATAGGA-C-GCAATCTTCAACCTACTCCACTACTGCCTAGGGTGA
* * * *
131 GAGGACTAATGGCTTAAATCTGCTTCTCCACTTTATTTGGAAGCTAAGATTCACAATCTTCGATC
64 GAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCACAATCTTCGATC
**
196 CGC-TCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTA
129 CGCAT-CACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACAGA
* * *
242 CTCCACTATTGCCTAGGGTGATAGGACGCAATCTTCAACCTACTCCACTATTGCCTAGGGTGATA
1 CTCCACTACTGCCTAGGGTGATAGGACGCAATCTTCAACCTACTCCACTACTGCCTAGGGTGAGA
* * *
307 GGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCGCCATCTTCGATCTG
66 GGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCACAATCTTCGATCCG
372 CATCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACAGA
131 CATCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACAGA
**
416 CTCCACTACTGTTTAGGGTGATAGGAC
1 CTCCACTACTGCCTAGGGTGATAGGAC
443 TAGGGTGATA
Statistics
Matches: 180, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
174 157 0.87
175 2 0.01
176 21 0.12
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (174 bp):
CTCCACTACTGCCTAGGGTGATAGGACGCAATCTTCAACCTACTCCACTACTGCCTAGGGTGAGA
GGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCACAATCTTCGATCCG
CATCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACAGA
Found at i:448 original size:14 final size:14
Alignment explanation
Indices: 429--458 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
419 CACTACTGTT
429 TAGGGTGATAGGAC
1 TAGGGTGATAGGAC
443 TAGGGTGATAGGAC
1 TAGGGTGATAGGAC
457 TA
1 TA
459 ATGGCTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.40, T:0.23
Consensus pattern (14 bp):
TAGGGTGATAGGAC
Found at i:531 original size:57 final size:57
Alignment explanation
Indices: 443--1134 Score: 1339
Period size: 57 Copynumber: 12.1 Consensus size: 57
433 GTGATAGGAC
*
443 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCACTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
500 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
557 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
614 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
671 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
728 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
785 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
842 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
899 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
956 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1013 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
** * *
1070 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACAGACTCCACTACTGTT
1 TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
1127 TAGGGTGA
1 TAGGGTGA
1135 CAGAATCTAT
Statistics
Matches: 630, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 630 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (57 bp):
TAGGGTGATAGGACTAATGGCTGAAATCTGCAATCTTCAACCTACTCCTCTACTGCT
Done.