Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5124.1
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: 32691
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:136 original size:81 final size:81
Alignment explanation
Indices: 1--673 Score: 1346
Period size: 81 Copynumber: 8.3 Consensus size: 81
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
66 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
82 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
147 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
163 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
228 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
244 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
309 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
325 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
390 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
406 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
471 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
487 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
552 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
568 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
1 ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
633 ATTATGGAAATCAGTC
66 ATTATGGAAATCAGTC
649 ATTTAATGATTTTAATTTTGAAGGT
1 ATTTAATGATTTTAATTTTGAAGGT
674 CATCACTAGT
Statistics
Matches: 592, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 592 1.00
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.47
Consensus pattern (81 bp):
ATTTAATGATTTTAATTTTGAAGGTTTTGGTGGGAGTGTAATTGTTTTTAAAGGATTTTGGTTAT
ATTATGGAAATCAGTC
Found at i:801 original size:33 final size:33
Alignment explanation
Indices: 764--833 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
754 GGGAAAGTTA
* *
764 ATTGGATGCATATAAAATTACTTGCTAAATTTT
1 ATTGGATACATATAAAACTACTTGCTAAATTTT
* * *
797 ATTGGTTATATATAAAACTACTTTCTAAATTTT
1 ATTGGATACATATAAAACTACTTGCTAAATTTT
830 ATTG
1 ATTG
834 AAAGTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (33 bp):
ATTGGATACATATAAAACTACTTGCTAAATTTT
Found at i:9709 original size:37 final size:37
Alignment explanation
Indices: 9663--9742 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
9653 AATGATGTTA
*
9663 ATGCCTAAGTTAATCTAAAGTAAGTTTATAAACACAT
1 ATGCATAAGTTAATCTAAAGTAAGTTTATAAACACAT
9700 ATGCATAAGTTAATCTAAAGTAAGTTTATAAACACAT
1 ATGCATAAGTTAATCTAAAGTAAGTTTATAAACACAT
9737 ATGCAT
1 ATGCAT
9743 GTAATGGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (37 bp):
ATGCATAAGTTAATCTAAAGTAAGTTTATAAACACAT
Found at i:11720 original size:8 final size:8
Alignment explanation
Indices: 11707--11759 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
11697 ACCCATACCC
11707 GAAGCCCA
1 GAAGCCCA
11715 GAAGCCCA
1 GAAGCCCA
*
11723 -AAACCCA
1 GAAGCCCA
11730 GAAGCCCA
1 GAAGCCCA
*
11738 -AAACCCA
1 GAAGCCCA
*
11745 -AAACCCA
1 GAAGCCCA
11752 GAAGCCCA
1 GAAGCCCA
11760 AAACCCACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 19 0.49
8 20 0.51
ACGTcount: A:0.45, C:0.40, G:0.15, T:0.00
Consensus pattern (8 bp):
GAAGCCCA
Found at i:11728 original size:22 final size:22
Alignment explanation
Indices: 11695--11766 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
11685 ACCCATTTTC
*
11695 AAACCC-ATACCC-GAAGCCCA
1 AAACCCAAAACCCAGAAGCCCA
*
11715 GAAGCCCAAAACCCAGAAGCCCA
1 -AAACCCAAAACCCAGAAGCCCA
11738 AAACCCAAAACCCAGAAGCCCA
1 AAACCCAAAACCCAGAAGCCCA
11760 AAACCCA
1 AAACCCA
11767 CCTAATCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 5 0.11
22 33 0.72
23 8 0.17
ACGTcount: A:0.46, C:0.42, G:0.11, T:0.01
Consensus pattern (22 bp):
AAACCCAAAACCCAGAAGCCCA
Found at i:11744 original size:7 final size:7
Alignment explanation
Indices: 11719--11766 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
11709 AGCCCAGAAG
11719 CCCAAAA
1 CCCAAAA
*
11726 CCCAGAAG
1 CCCA-AAA
11734 CCCAAAA
1 CCCAAAA
11741 CCCAAAA
1 CCCAAAA
*
11748 CCCAGAAG
1 CCCA-AAA
11756 CCCAAAA
1 CCCAAAA
11763 CCCA
1 CCCA
11767 CCTAATCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
7 23 0.66
8 12 0.34
ACGTcount: A:0.48, C:0.44, G:0.08, T:0.00
Consensus pattern (7 bp):
CCCAAAA
Found at i:11766 original size:15 final size:15
Alignment explanation
Indices: 11711--11744 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
11701 ATACCCGAAG
11711 CCCAGAAGCCCAAAA
1 CCCAGAAGCCCAAAA
11726 CCCAGAAGCCCAAAA
1 CCCAGAAGCCCAAAA
11741 CCCA
1 CCCA
11745 AAACCCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.44, G:0.12, T:0.00
Consensus pattern (15 bp):
CCCAGAAGCCCAAAA
Found at i:12915 original size:21 final size:21
Alignment explanation
Indices: 12874--12915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12864 TCTAATATAA
* *
12874 ATATATATATCATATAGGTTT
1 ATATACATATCATACAGGTTT
*
12895 ATATACATATCATACATGTTT
1 ATATACATATCATACAGGTTT
12916 CTTTATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATACATATCATACAGGTTT
Found at i:13112 original size:11 final size:11
Alignment explanation
Indices: 13096--13160 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
13086 TTATTTTCAA
13096 TATGTATATAT
1 TATGTATATAT
*
13107 TATGTAAATATTT
1 TATGT--ATATAT
13120 TGATGT-TATAT
1 T-ATGTATATAT
* *
13131 TATATATGTAT
1 TATGTATATAT
* *
13142 TTTTTATATAT
1 TATGTATATAT
13153 TATGTATA
1 TATGTATA
13161 CATATATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
10 3 0.07
11 28 0.68
13 6 0.15
14 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (11 bp):
TATGTATATAT
Found at i:19178 original size:15 final size:15
Alignment explanation
Indices: 19160--19218 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
19150 GAAGCCCAGA
*
19160 ATAAAGAAATCCAAG
1 ATAAGGAAATCCAAG
19175 ATAAGGAAATCCATA-
1 ATAAGGAAATCCA-AG
*
19190 ATAAGGAAATCCATG
1 ATAAGGAAATCCAAG
19205 ATAAGGAAATCCAA
1 ATAAGGAAATCCAA
19219 TTTACAGCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
15 38 0.97
16 1 0.03
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:19193 original size:30 final size:30
Alignment explanation
Indices: 19159--19217 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
19149 AGAAGCCCAG
19159 AATAAAGAAATCCAAGATAAGGAAATCCAT
1 AATAAAGAAATCCAAGATAAGGAAATCCAT
* *
19189 AATAAGGAAATCCATGATAAGGAAATCCA
1 AATAAAGAAATCCAAGATAAGGAAATCCA
19218 ATTTACAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17
Consensus pattern (30 bp):
AATAAAGAAATCCAAGATAAGGAAATCCAT
Found at i:26996 original size:25 final size:25
Alignment explanation
Indices: 26968--27017 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
26958 TGAGACAGAG
26968 TTGGAGTGATTCCAGACTCCCCTGT
1 TTGGAGTGATTCCAGACTCCCCTGT
26993 TTGGAGTGATTCCAGACTCCCCTGT
1 TTGGAGTGATTCCAGACTCCCCTGT
27018 CTCAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (25 bp):
TTGGAGTGATTCCAGACTCCCCTGT
Done.