Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1578
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: 60656
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Found at i:15316 original size:84 final size:84
Alignment explanation
Indices: 15213--15376 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 84
15203 GGGTCTCAAC
*
15213 TGACAGCTAACTAGTGTCAAACCA-AATTTCAGC-CGTTTGTTGACAATCAACTGTCAGTAAAGA
1 TGACAGCTAACTAGTGTCAAACCAGAATCTCA-CAC-TTTGTTGACAATCAACTGTCAGTAAAGA
*
15276 ACCGGTTAATCAACTGTCAGA
64 ACCGGTTAACCAACTGTCAGA
* * * * * *
15297 TGACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTTGTTGACAATCAGCTGTTAGTTAAGAAC
1 TGACAGCTAACTAGTGTCAAACCAGAATCTCACACTTTGTTGACAATCAACTGTCAGTAAAGAAC
15362 CGGTTAACCAACTGT
66 CGGTTAACCAACTGT
15377 TAACTAACAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 64 0.91
85 6 0.09
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (84 bp):
TGACAGCTAACTAGTGTCAAACCAGAATCTCACACTTTGTTGACAATCAACTGTCAGTAAAGAAC
CGGTTAACCAACTGTCAGA
Found at i:15357 original size:157 final size:155
Alignment explanation
Indices: 15077--15357 Score: 420
Period size: 157 Copynumber: 1.8 Consensus size: 155
15067 AATACCTCTG
* * * ** *
15077 AACCACAATTTAGTCGTTTGTTGACAATCAGCCGTTAGTTCGACCGGTTAACCAGCTGTCAGATG
1 AACCACAATTTAGCCGTTTGTTGACAATCAACCGTCAGTAAGACCGGTTAACCAACTGTCAGATG
* *
15142 ACAGCTGAGTAGTGTCAAACCAGAATTTGACACTTGGTTGACAATCAGCTGATGGTTAATCGGGT
66 ACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTGGTTGACAATCAGCTGATAGTTAATCGGGT
15207 CTCAACTGACAGCTAACTAGTGTCA
131 CTCAACTGACAGCTAACTAGTGTCA
* *
15232 AACCA-AATTTCAGCCGTTTGTTGACAATCAACTGTCAGTAAAGAACCGGTTAATCAACTGTCAG
1 AACCACAATTT-AGCCGTTTGTTGACAATCAACCGTCAGT-AAG-ACCGGTTAACCAACTGTCAG
* *
15296 ATGACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTTGTTGACAATCAGCTGTTAGTTAA
63 ATGACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTGGTTGACAATCAGCTGATAGTTAA
15358 GAACCGGTTA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
154 5 0.05
155 29 0.26
156 1 0.01
157 76 0.68
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (155 bp):
AACCACAATTTAGCCGTTTGTTGACAATCAACCGTCAGTAAGACCGGTTAACCAACTGTCAGATG
ACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTGGTTGACAATCAGCTGATAGTTAATCGGGT
CTCAACTGACAGCTAACTAGTGTCA
Found at i:25469 original size:84 final size:84
Alignment explanation
Indices: 25366--25529 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 84
25356 GGGTCTCAAC
*
25366 TGACAGCTAACTAGTGTCAAACCA-AATTTCAGC-CGTTTGTTGACAATCAACTGTCAGTAAAGA
1 TGACAGCTAACTAGTGTCAAACCAGAATCTCA-CAC-TTTGTTGACAATCAACTGTCAGTAAAGA
*
25429 ACCGGTTAATCAACTGTCAGA
64 ACCGGTTAACCAACTGTCAGA
* * * * * *
25450 TGACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTTGTTGACAATCAGCTGTTAGTTAAGAAC
1 TGACAGCTAACTAGTGTCAAACCAGAATCTCACACTTTGTTGACAATCAACTGTCAGTAAAGAAC
25515 CGGTTAACCAACTGT
66 CGGTTAACCAACTGT
25530 TAACTAACAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 64 0.91
85 6 0.09
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (84 bp):
TGACAGCTAACTAGTGTCAAACCAGAATCTCACACTTTGTTGACAATCAACTGTCAGTAAAGAAC
CGGTTAACCAACTGTCAGA
Found at i:25510 original size:157 final size:155
Alignment explanation
Indices: 25230--25510 Score: 420
Period size: 157 Copynumber: 1.8 Consensus size: 155
25220 AATACCTCTG
* * * ** *
25230 AACCACAATTTAGTCGTTTGTTGACAATCAGCCGTTAGTTCGACCGGTTAACCAGCTGTCAGATG
1 AACCACAATTTAGCCGTTTGTTGACAATCAACCGTCAGTAAGACCGGTTAACCAACTGTCAGATG
* *
25295 ACAGCTGAGTAGTGTCAAACCAGAATTTGACACTTGGTTGACAATCAGCTGATGGTTAATCGGGT
66 ACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTGGTTGACAATCAGCTGATAGTTAATCGGGT
25360 CTCAACTGACAGCTAACTAGTGTCA
131 CTCAACTGACAGCTAACTAGTGTCA
* *
25385 AACCA-AATTTCAGCCGTTTGTTGACAATCAACTGTCAGTAAAGAACCGGTTAATCAACTGTCAG
1 AACCACAATTT-AGCCGTTTGTTGACAATCAACCGTCAGT-AAG-ACCGGTTAACCAACTGTCAG
* *
25449 ATGACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTTGTTGACAATCAGCTGTTAGTTAA
63 ATGACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTGGTTGACAATCAGCTGATAGTTAA
25511 GAACCGGTTA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
154 5 0.05
155 29 0.26
156 1 0.01
157 76 0.68
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (155 bp):
AACCACAATTTAGCCGTTTGTTGACAATCAACCGTCAGTAAGACCGGTTAACCAACTGTCAGATG
ACAGCTGAGTAGTGTCAAACCAGAATCTGACACTTGGTTGACAATCAGCTGATAGTTAATCGGGT
CTCAACTGACAGCTAACTAGTGTCA
Found at i:35628 original size:84 final size:85
Alignment explanation
Indices: 35408--35618 Score: 322
Period size: 84 Copynumber: 2.5 Consensus size: 85
35398 AATTTAGTCG
* * * *
35408 TTTGTTGACAATCAGCCGTTAGTT-CG-ACCGGTTAACCAGCTGTCAGATGACAGCTGAGTAGTG
1 TTTGTTGACAATCAGCTGTTAGTTAAGAACCGGTTAACCAACTGTCAGATAACAGCTGAGTAGTG
35471 TCAAACCAGAATT-TGACAC
66 TCAAACCAGAATTCTGACAC
* * *
35490 TTGGTTGACAATCAGCTGTCAGTTAAGAACCGGTTAATCAACTGTCAGATAACAGCTGAGTAGTG
1 TTTGTTGACAATCAGCTGTTAGTTAAGAACCGGTTAACCAACTGTCAGATAACAGCTGAGTAGTG
35555 TCAAACCA-AATTCTGACAC
66 TCAAACCAGAATTCTGACAC
*
35574 TTTGTTGACAATCAGCTGTTGGTTAAGAACCGGTTAACCAACTGT
1 TTTGTTGACAATCAGCTGTTAGTTAAGAACCGGTTAACCAACTGT
35619 TAACTAACAG
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
82 21 0.18
83 5 0.04
84 89 0.77
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (85 bp):
TTTGTTGACAATCAGCTGTTAGTTAAGAACCGGTTAACCAACTGTCAGATAACAGCTGAGTAGTG
TCAAACCAGAATTCTGACAC
Done.