Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1036
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: 32799
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1403 original size:23 final size:22
Alignment explanation
Indices: 1377--1430 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1367 TTTTCTTTTT
*
1377 TTTTTTTTTCTTATTTTTATCTG
1 TTTTTTTTT-TTATTTTTATCTA
* *
1400 TTTTTTCTTTTTCTTTTTTTCTA
1 TTTTTT-TTTTTATTTTTATCTA
1423 TTTTTTTT
1 TTTTTTTT
1431 CATTTATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.06, C:0.09, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTTTTTTTTATTTTTATCTA
Found at i:1429 original size:26 final size:24
Alignment explanation
Indices: 1366--1430 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
1356 AAGGGCTTTC
*
1366 TTTTTCTTTTTTTTTTTTTTCTTA
1 TTTTTATTTTTTTTTTTTTTCTTA
* *
1390 TTTTTATCTGTTTTTTCTTTTTCTTT
1 TTTTTAT-T-TTTTTTTTTTTTCTTA
1416 TTTTCTATTTTTTTT
1 TTTT-TATTTTTTTT
1431 CATTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.17
25 7 0.20
26 19 0.54
27 3 0.09
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.85
Consensus pattern (24 bp):
TTTTTATTTTTTTTTTTTTTCTTA
Found at i:4895 original size:23 final size:22
Alignment explanation
Indices: 4843--4895 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4833 TTTCCGTCTT
*
4843 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4865 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4888 TTTCTTTT
1 TTTCTTTT
4896 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:7747 original size:14 final size:14
Alignment explanation
Indices: 7718--7753 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
7708 AATGTGAACT
7718 TAATTAAAACATAGC
1 TAATT-AAACATAGC
*
7733 TAATTAAAGATAGC
1 TAATTAAACATAGC
7747 TAATTAA
1 TAATTAA
7754 TGAACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (14 bp):
TAATTAAACATAGC
Found at i:9088 original size:46 final size:46
Alignment explanation
Indices: 9023--9433 Score: 515
Period size: 46 Copynumber: 9.0 Consensus size: 46
9013 TTATCTTCGA
* * * *
9023 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* * ** *
9069 CAGGTTGCCATGGAATCTTTCAACCATGGTCTTGTTTATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* **
9115 --TGCATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATG--TTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
9160 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
9206 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
9252 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*** * * *
9298 TGCGTTGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
9344 CATGTTGCTATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
9390 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
9434 TTTAGAAAGC
Statistics
Matches: 314, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
44 1 0.00
45 41 0.13
46 270 0.86
47 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:15138 original size:20 final size:20
Alignment explanation
Indices: 15115--15161 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15105 GGGTTAAGAT
*
15115 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
15135 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
15155 TGAGCTG
1 TGAGCTG
15162 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:16879 original size:47 final size:46
Alignment explanation
Indices: 16828--16929 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
16818 TTGTCTTTTC
* *
16828 TTTCTTTTCAATTT-TCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTCAATTTCTCTCTCTTT--TCACATCCTTT-TTCAATCTCAA
* *
16875 TTTCTTTTTCGATTTCTTTCTCTTTTCACATCCTTTTTCAATCTCAA
1 TTTC-TTTTCAATTTCTCTCTCTTTTCACATCCTTTTTCAATCTCAA
16922 TTTCTTTT
1 TTTCTTTT
16930 TCCATGACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
46 4 0.08
47 24 0.50
48 13 0.27
49 7 0.15
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.59
Consensus pattern (46 bp):
TTTCTTTTCAATTTCTCTCTCTTTTCACATCCTTTTTCAATCTCAA
Found at i:17008 original size:12 final size:12
Alignment explanation
Indices: 16975--17048 Score: 51
Period size: 13 Copynumber: 5.9 Consensus size: 12
16965 TTTTCACTTG
16975 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
16986 AGCTCTCTTTCA
1 ATTTCTTTTTCA
*
16998 ATTTCTTTTTCGC
1 ATTTCTTTTTC-A
*
17011 TTTTCTTTTTCA
1 ATTTCTTTTTCA
17023 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
*
17038 TTTTCTTTTTC
1 ATTTCTTTTTC
17049 TCTCACTTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
11 3 0.06
12 16 0.34
13 17 0.36
14 7 0.15
15 4 0.09
ACGTcount: A:0.11, C:0.22, G:0.03, T:0.65
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:17017 original size:13 final size:13
Alignment explanation
Indices: 16993--17048 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
16983 TCAAGCTCTC
16993 TTTCAA-TTTCTT
1 TTTCAATTTTCTT
**
17005 TTTCGCTTTTCTT
1 TTTCAATTTTCTT
17018 TTTCAATTTTCTTT
1 TTTCAATTTTC-TT
17032 TCTTC-ATTTTCTT
1 T-TTCAATTTTCTT
17045 TTTC
1 TTTC
17049 TCTCACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 7 0.19
13 18 0.49
14 9 0.24
15 3 0.08
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTCAATTTTCTT
Found at i:17083 original size:40 final size:41
Alignment explanation
Indices: 16991--17129 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 41
16981 TTTCAAGCTC
**
16991 TCTTTCAATTTCTTTTTCGCTTTTCTTTTTCAATTTTCTTT
1 TCTTTCAATTTCTTTTTCGCTTCACTTTTTCAATTTTCTTT
* * *
17032 TC-TTCATTTTCTTTTTCTC-TCACTTTTTCGA-TTTCTTT
1 TCTTTCAATTTCTTTTTCGCTTCACTTTTTCAATTTTCTTT
* *
17070 TCTTTGCAATTTCTTTTTTCTTCTTC-TTCTTTTC--TTTT-TGTT
1 TCTTT-CAATTTC-TTTTTC-GCTTCACT-TTTTCAATTTTCT-TT
17112 TCTTTCAATTTCTTTTTC
1 TCTTTCAATTTCTTTTTC
17130 AATCTCTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 17
0.78 0.07 0.16
Matches are distributed among these distances:
38 9 0.11
39 11 0.13
40 27 0.33
41 16 0.19
42 13 0.16
43 7 0.08
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (41 bp):
TCTTTCAATTTCTTTTTCGCTTCACTTTTTCAATTTTCTTT
Found at i:17128 original size:21 final size:20
Alignment explanation
Indices: 17067--17128 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
17057 TTTCGATTTC
17067 TTTTCTTTGCAATTTCTTTTT
1 TTTTCTTT-CAATTTCTTTTT
* *
17088 TCTTCTTCTTC-TTTTCTTTTT
1 TTTTC-T-TTCAATTTCTTTTT
*
17109 GTTTCTTTCAATTTCTTTTT
1 TTTTCTTTCAATTTCTTTTT
17129 CAATCTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 16 0.48
22 2 0.06
23 2 0.06
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTTCTTTCAATTTCTTTTT
Found at i:18186 original size:30 final size:28
Alignment explanation
Indices: 18152--18214 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
18142 TTAAACTTGA
**
18152 TTTTTTTGCTCACCTTTTTTTTTCTTTTCT
1 TTTTTTTGCTC-CCTTTTTTTCACTTTT-T
*
18182 TTTTTTTGCTCGCTTTTTTTCACTTTTT
1 TTTTTTTGCTCCCTTTTTTTCACTTTTT
18210 TTTTT
1 TTTTT
18215 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 6 0.20
29 13 0.43
30 11 0.37
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTGCTCCCTTTTTTTCACTTTTT
Found at i:19765 original size:20 final size:20
Alignment explanation
Indices: 19742--19788 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19732 GGGTTAAGAT
*
19742 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
19762 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
19782 TGAGCTG
1 TGAGCTG
19789 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:20905 original size:30 final size:30
Alignment explanation
Indices: 20871--20957 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
20861 AGCTCACTCC
*
20871 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * *
20901 TAGCTCAACTTTAGCTTAAGAGTTTAACCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
20931 TAGCTCAACTTTAGCTCACGAGCTAAA
1 TAGCTCAACTTTAGCTCACGAGCTAAA
20958 GCTGATACGG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 42 0.89
31 5 0.11
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Done.