Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1193
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: 28584
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Found at i:735 original size:19 final size:19
Alignment explanation
Indices: 713--763 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
703 TAATCTTTAG
* *
713 GATATCCAATCTTAGATAT
1 GATATACAATCTTAGAGAT
732 GATATACAATCTTAGAGAT
1 GATATACAATCTTAGAGAT
*
751 GATATGCAATCTT
1 GATATACAATCTT
764 GTAATCTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (19 bp):
GATATACAATCTTAGAGAT
Found at i:7601 original size:27 final size:27
Alignment explanation
Indices: 7571--7748 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
7561 ATATTGAGTC
* * * *
7571 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
7598 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
7625 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
7653 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
7680 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
7707 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
7734 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
7749 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:7710 original size:82 final size:81
Alignment explanation
Indices: 7592--7747 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
7582 TGCTATATAA
* *
7592 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
7657 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
7674 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
7738 CACTTAGTGC
65 CACTTAGTGC
7748 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:15649 original size:27 final size:27
Alignment explanation
Indices: 15619--15796 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15609 ATATTGAGTC
* * * *
15619 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
15646 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
15673 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
15701 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
15728 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
15755 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
15782 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15797 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:15758 original size:82 final size:81
Alignment explanation
Indices: 15640--15795 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
15630 TGCTATATAA
* *
15640 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
15705 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
15722 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
15786 CACTTAGTGC
65 CACTTAGTGC
15796 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:26843 original size:8 final size:8
Alignment explanation
Indices: 26830--26881 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
26820 AAACAGAGGA
26830 AAAAAAAG
1 AAAAAAAG
26838 AAAAAAAAG
1 -AAAAAAAG
26847 AAAAAAAAG
1 -AAAAAAAG
*
26856 AAAAAGAG
1 AAAAAAAG
* *
26864 AGAAAATG
1 AAAAAAAG
*
26872 AATAAAAG
1 AAAAAAAG
26880 AA
1 AA
26882 GGAGAGGCGC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
8 19 0.53
9 17 0.47
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:26869 original size:10 final size:9
Alignment explanation
Indices: 26828--26860 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
26818 AAAAACAGAG
26828 GAAAAAAAA
1 GAAAAAAAA
26837 GAAAAAAAA
1 GAAAAAAAA
26846 GAAAAAAAA
1 GAAAAAAAA
26855 GAAAAA
1 GAAAAA
26861 GAGAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Done.