Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4411
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: 14924
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:4942 original size:26 final size:27
Alignment explanation
Indices: 4909--5086 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
4899 TTGATATCTG
* * *
4909 GACCGAAATACCCCCGTAGGGTAGAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * * *
4936 -ACTGAAATACCCCAGTATGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
4962 GACCGTAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
4989 GACCGTAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
5016 GACCGTAATACCCCTATAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * * * * * *
5043 AATCGTAATATCCTTGTAAGATAAAAG
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
5070 GACCGTAATGCCCCTGT
1 GACCGTAATACCCCTGT
5087 CGTGACATGA
Statistics
Matches: 126, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 22 0.17
27 104 0.83
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
GACCGTAATACCCCTGTAGGGTAAAAT
Found at i:8774 original size:50 final size:49
Alignment explanation
Indices: 8707--9083 Score: 420
Period size: 50 Copynumber: 7.6 Consensus size: 49
8697 ACTGCCAATG
* * * ** * *
8707 CCATATCCCAGATATGGTCTTACACGGGAGTTCTCATATCAGTGCTCATA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC-CATA
** * *
8757 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC-ATA
* *
8807 CCATGTCCCAAACATAGTCTTACATGGGACCTCTCATCTCGGTGCC-TA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATA
*
8855 CGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCA-A
1 --CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATA
* * * * *
8905 CGCCATGTCCCAAACATGGTCTTACATGAGACTTCTCATCCCGGTGCCAATG
1 --CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC-ATA
* * *
8957 CCATGTCCCAAACATGGTCTTACATGGGACCTTTCATCACGGTGCCA-A
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATA
*
9005 CGCCATGTCCCAGACATTGTCTTACATGGGACCTCTCATCTCGGTGCCA-A
1 --CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATA
9055 CGCTATGTCCCAGACATGGTCTTACATGG
1 C-C-ATGTCCCAGACATGGTCTTACATGG
9084 CTCACATATT
Statistics
Matches: 286, Mismatches: 31, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
48 2 0.01
49 3 0.01
50 280 0.98
51 1 0.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATA
Found at i:8830 original size:100 final size:99
Alignment explanation
Indices: 8658--9083 Score: 482
Period size: 100 Copynumber: 4.3 Consensus size: 99
8648 CATGCCAAAG
* * ** * * * * * *
8658 CCATGTCCCAGACATGGTCTTACGTGGGA--TGTTTTCTGTACTGCCAATGCCATATCCCAGATA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CAGTGCCAACGCCATGTCCCAAACA
* ** * *
8721 TGGTCTTACACGGGAGTTCTCATATCAGTGCTCATA
65 TGGTCTTACATGGGACCTCTCATCTCGGTGC-CATA
** *
8757 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAATGCCATGTCCCAAACAT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACAT
*
8822 AGTCTTACATGGGACCTCTCATCTCGGTGCC-TA
66 GGTCTTACATGGGACCTCTCATCTCGGTGCCATA
* *
8855 CGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
1 --CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAAC
* * * *
8920 ATGGTCTTACATGAGACTTCTCATCCCGGTGCCAATG
64 ATGGTCTTACATGGGACCTCTCATCTCGGTGCC-ATA
* * * * *
8957 CCATGTCCCAAACATGGTCTTACATGGGACCTTTCATCACGGTGCCAACGCCATGTCCCAGACAT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACAT
*
9022 TGTCTTACATGGGACCTCTCATCTCGGTGCCA-A
66 GGTCTTACATGGGACCTCTCATCTCGGTGCCATA
9055 CGCTATGTCCCAGACATGGTCTTACATGG
1 C-C-ATGTCCCAGACATGGTCTTACATGG
9084 CTCACATATT
Statistics
Matches: 283, Mismatches: 36, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
98 3 0.01
99 31 0.11
100 243 0.86
101 5 0.02
102 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (99 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACAT
GGTCTTACATGGGACCTCTCATCTCGGTGCCATA
Found at i:9081 original size:150 final size:149
Alignment explanation
Indices: 8650--9082 Score: 541
Period size: 150 Copynumber: 2.9 Consensus size: 149
8640 GATAATAACA
* * * ** * * *
8650 TGCCAAAGCCATGTCCCAGACATGGTCTTACGTGGGATGTTTTC-TGTAC--TGCCAATGCCATA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA-CCTTTCAT-CACGGTGCCAACGCCATG
* * ** * *
8712 TCCCAGATATGGTCTTACACGGGAGTTCTCATATCAGTGCTCATAC-CATGTCCCAGACATGGTC
64 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC-CA-ACGCATGTCCCAGACATGGTC
** * *
8776 TTACGGGGGACCTCTCATCTCAG
127 TTACATGAGACCTCTCATCCCAG
* * * *
8799 TGCCAATGCCATGTCCCAAACATAGTCTTACATGGGACCTCTCATCTCGGTGCCTACGCCATGTC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTTTCATCACGGTGCCAACGCCATGTC
* *
8864 CCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACATGGTCTTA
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG-CATGTCCCAGACATGGTCTTA
* *
8929 CATGAGACTTCTCATCCCGG
130 CATGAGACCTCTCATCCCAG
8949 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTTTCATCACGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTTTCATCACGGTGCCAACGCCATGTC
*
9014 CCAGACATTGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCTATGTCCCAGACATGGTCTTA
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC-ATGTCCCAGACATGGTCTTA
9079 CATG
130 CATG
9083 GCTCACATAT
Statistics
Matches: 245, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
148 6 0.02
149 37 0.15
150 202 0.82
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (149 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTTTCATCACGGTGCCAACGCCATGTC
CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCATGTCCCAGACATGGTCTTAC
ATGAGACCTCTCATCCCAG
Done.