Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2905
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: 22770
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:3899 original size:27 final size:27
Alignment explanation
Indices: 3869--4046 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3859 ATATTGAGTC
* * * *
3869 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
3896 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3923 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
3951 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
3978 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
4005 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
4032 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4047 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:4008 original size:82 final size:81
Alignment explanation
Indices: 3890--4045 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3880 TGCTATATAA
* *
3890 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
3955 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
3972 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
4036 CACTTAGTGC
65 CACTTAGTGC
4046 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:6122 original size:42 final size:42
Alignment explanation
Indices: 6060--6399 Score: 163
Period size: 48 Copynumber: 7.6 Consensus size: 42
6050 AACTATTGTT
* *
6060 TTACAC-AAAGTCTCACATCGATGCCATGTCCCAGACATGGTC
1 TTACACGAAA-TCTCATATCGATGCCATATCCCAGACATGGTC
* * **
6102 TTATACGAAATCACATATCGATGCCGCATCCCAGACATGGTC
1 TTACACGAAATCTCATATCGATGCCATATCCCAGACATGGTC
* * * * * * *
6144 TTACACGAAATTTCATACCAAAGCCATATCCTAGATATGGTA
1 TTACACGAAATCTCATATCGATGCCATATCCCAGACATGGTC
* * *
6186 TTACACGTAATCTCATATCGATGCCGATGTCATATCGCAGATATGGTC
1 TTACACGAAATCTCATATCGATG-C-----CATATCCCAGACATGGTC
* *
6234 --ACAC-AAGATCTCATATTGATGCTGATGCCATATCCCAGATATAGTC
1 TTACACGAA-ATCTC--A-T-AT-C-GATGCCATATCCCAGACATGGTC
* *
6280 TTACAC-AGGATCTCATATCGATGCTGATGCCATATCCCAGATATGGTC
1 TTACACGA-AATCTC--AT--AT-C-GATGCCATATCCCAGACATGGTC
* * *
6328 TTACAC-AGGATCTCATATTGATGCCGATATCATATCCCAGATATGGTC
1 TTACACGA-AATCTCATATCGATG-C-----CATATCCCAGACATGGTC
6376 TTACAC-AAGATCTCATATCGATGC
1 TTACACGAA-ATCTCATATCGATGC
6400 TGATGTCATA
Statistics
Matches: 240, Mismatches: 33, Indels: 45
0.75 0.10 0.14
Matches are distributed among these distances:
42 85 0.35
43 5 0.02
44 2 0.01
45 1 0.00
46 27 0.11
47 2 0.01
48 109 0.45
49 1 0.00
50 2 0.01
51 2 0.01
52 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
TTACACGAAATCTCATATCGATGCCATATCCCAGACATGGTC
Found at i:6303 original size:48 final size:48
Alignment explanation
Indices: 6166--6494 Score: 432
Period size: 48 Copynumber: 6.9 Consensus size: 48
6156 TCATACCAAA
* * * *
6166 GCCATATCCTAGATATGGTATTACAC-GTAATCTCATATCGATGCCGAT
1 GCCATATCCCAGATATGGTCTTACACAG-GATCTCATATCGATGCTGAT
* * * *
6214 GTCATATCGCAGATATGGTC--ACACAAGATCTCATATTGATGCTGAT
1 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGCTGAT
*
6260 GCCATATCCCAGATATAGTCTTACACAGGATCTCATATCGATGCTGAT
1 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGCTGAT
* *
6308 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATTGATGCCGAT
1 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGCTGAT
** *
6356 ATCATATCCCAGATATGGTCTTACACAAGATCTCATATCGATGCTGAT
1 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGCTGAT
* * *
6404 GTCATATCCCAGAT-TGGCCTTACACAAGATCTCATATCGATGCTGAT
1 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGCTGAT
** * *
6451 GCCATATCCTGGATATGGTCTTACACAGGGTCTCGTATCGATGC
1 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGC
6495 CATGTCCTAA
Statistics
Matches: 247, Mismatches: 30, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
46 38 0.15
47 43 0.17
48 166 0.67
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (48 bp):
GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGCTGAT
Found at i:6468 original size:143 final size:142
Alignment explanation
Indices: 6166--6495 Score: 493
Period size: 143 Copynumber: 2.3 Consensus size: 142
6156 TCATACCAAA
* * * *
6166 GCCATATCCTAGATATGGTATTACAC-GTAATCTCATATCGATGCCGATGTCATATCGCAGATAT
1 GCCATATCCTAGATATGGTCTTACACAG-GATCTCATATCGATGCCGATATCATATCCCAGATAT
* * *
6230 GGTCACACAAGATCTCATATTGATGCTGATGCCATATCCCAGATATAGTCTTACACAGGATCTCA
65 GGTCACACAAGATCTCATATCGATGCTGATGCCATATCCCAGATATAGCCTTACACAAGATCTCA
6295 TATCGATGCTGAT
130 TATCGATGCTGAT
* *
6308 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATTGATGCCGATATCATATCCCAGATATG
1 GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATATCATATCCCAGATATG
* *
6373 GTCTTACACAAGATCTCATATCGATGCTGATGTCATATCCCAGAT-TGGCCTTACACAAGATCTC
66 GTC--ACACAAGATCTCATATCGATGCTGATGCCATATCCCAGATATAGCCTTACACAAGATCTC
6437 ATATCGATGCTGAT
129 ATATCGATGCTGAT
* * *
6451 GCCATATCCTGGATATGGTCTTACACAGGGTCTCGTATCGATGCC
1 GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCC
6496 ATGTCCTAAG
Statistics
Matches: 169, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
142 60 0.36
143 71 0.42
144 38 0.22
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (142 bp):
GCCATATCCTAGATATGGTCTTACACAGGATCTCATATCGATGCCGATATCATATCCCAGATATG
GTCACACAAGATCTCATATCGATGCTGATGCCATATCCCAGATATAGCCTTACACAAGATCTCAT
ATCGATGCTGAT
Found at i:6573 original size:37 final size:37
Alignment explanation
Indices: 6507--6664 Score: 230
Period size: 37 Copynumber: 4.3 Consensus size: 37
6497 TGTCCTAAGC
* *
6507 ATGGTCTTACACGT-ATCACGATGCCATAGCCCCGCT
1 ATGGTCTTACATGTCATCACGATGCCATAGCCCAGCT
* *
6543 ATGGTCTTACATGTCATCATGATGCCATAGCCTAGCT
1 ATGGTCTTACATGTCATCACGATGCCATAGCCCAGCT
6580 ATGGTCTTACATGTCATCACGATGCCATAGCCCAGCT
1 ATGGTCTTACATGTCATCACGATGCCATAGCCCAGCT
** *
6617 ATGGTCTTACA-CACTATTACGATGCCATAGCCCAGCT
1 ATGGTCTTACATGTC-ATCACGATGCCATAGCCCAGCT
6654 ATGGTCTTACA
1 ATGGTCTTACA
6665 CGTACCACAT
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
36 14 0.13
37 97 0.87
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (37 bp):
ATGGTCTTACATGTCATCACGATGCCATAGCCCAGCT
Found at i:6618 original size:74 final size:73
Alignment explanation
Indices: 6489--6668 Score: 240
Period size: 74 Copynumber: 2.5 Consensus size: 73
6479 GGTCTCGTAT
*
6489 CGATGCCAT-GTCCTAAGC-ATGGTCTTACACGTATCACGATGCCATAGCCCCGCTATGGTCTTA
1 CGATGCCATAG-CCT-AGCTATGGTCTTACACGTATCACGATGCCATAGCCCAGCTATGGTCTTA
**
6552 CA-TGTCATCA
64 CACACT-ATCA
* *
6562 TGATGCCATAGCCTAGCTATGGTCTTACATGTCATCACGATGCCATAGCCCAGCTATGGTCTTAC
1 CGATGCCATAGCCTAGCTATGGTCTTACACGT-ATCACGATGCCATAGCCCAGCTATGGTCTTAC
*
6627 ACACTATTA
65 ACACTATCA
*
6636 CGATGCCATAGCCCAGCTATGGTCTTACACGTA
1 CGATGCCATAGCCTAGCTATGGTCTTACACGTA
6669 CCACATGTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
72 3 0.03
73 25 0.27
74 65 0.69
75 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (73 bp):
CGATGCCATAGCCTAGCTATGGTCTTACACGTATCACGATGCCATAGCCCAGCTATGGTCTTACA
CACTATCA
Found at i:11491 original size:28 final size:28
Alignment explanation
Indices: 11459--11528 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
11449 ATAGTAAGTC
11459 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
11487 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
11515 CGCACACTTAGTGC
1 CGCACACTTAGTGC
11529 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:14997 original size:27 final size:27
Alignment explanation
Indices: 14967--15144 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
14957 ATATTGAGTC
* * *
14967 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
14994 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
15021 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
15049 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
15076 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
15103 CGCACACTTAGTGCAACATATTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
15130 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15145 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 107 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:15080 original size:82 final size:81
Alignment explanation
Indices: 14988--15143 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
14978 TGCTATATAA
* *
14988 TCAACTCGCACACTTAGTGC-TACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
15052 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * ** *
15070 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATATTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
15135 ACTTAGTGC
66 ACTTAGTGC
15144 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.