Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1948
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: 23904
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Found at i:5209 original size:21 final size:24
Alignment explanation
Indices: 5162--5210 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5152 ACACCTCTCA
5162 ATAACATATACATACAAAATGATT
1 ATAACATATACATACAAAATGATT
*
5186 ATAACATATGC-T-CAAAAT-ATT
1 ATAACATATACATACAAAATGATT
5207 ATAA
1 ATAA
5211 GCCATTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 1 0.04
24 10 0.42
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAACATATACATACAAAATGATT
Found at i:5841 original size:40 final size:40
Alignment explanation
Indices: 5712--5927 Score: 350
Period size: 39 Copynumber: 5.5 Consensus size: 40
5702 CAACCAAGTA
* *
5712 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
5751 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5790 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5830 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
5870 CCTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
5928 TTATCATCGA
Statistics
Matches: 167, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
39 89 0.53
40 78 0.47
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:5842 original size:79 final size:78
Alignment explanation
Indices: 5712--5931 Score: 361
Period size: 79 Copynumber: 2.8 Consensus size: 78
5702 CAACCAAGTA
* *
5712 CCTTCGGGATTTAGCCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGT
1 CCTTCGGGACTTAGCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGT
5777 AACTCGCAC-AATG
65 AACTCGCACAAATG
*
5790 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAG-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
5855 TAACTCGCACAAATG
64 TAACTCGCACAAATG
*
5870 CCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
5932 CATCGAATAT
Statistics
Matches: 133, Mismatches: 6, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
78 14 0.11
79 101 0.76
80 18 0.14
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
ACTCGCACAAATG
Found at i:11829 original size:32 final size:34
Alignment explanation
Indices: 11775--11839 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
11765 TTTAGTGATT
11775 TTTCAAATCACATCACTGCTGCT-TCAGCATCTG
1 TTTCAAATCACATCACTGCTGCTGTCAGCATCTG
11808 TTTCAAATCACA-CACTGCTGCTGTCAGCATCT
1 TTTCAAATCACATCACTGCTGCTGTCAGCATCT
11840 ATTTTTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 10 0.32
33 21 0.68
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (34 bp):
TTTCAAATCACATCACTGCTGCTGTCAGCATCTG
Found at i:12608 original size:40 final size:40
Alignment explanation
Indices: 12539--12762 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 40
12529 AAACCAAGTA
* * *
12539 CCTTCGGGATTTAG-CCGGATATCGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
12578 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
12618 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
12658 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TA--ACTCGCACAAATG
*
12701 CCTTC-GGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12740 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
12763 CATCCGAATA
Statistics
Matches: 160, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
39 29 0.18
40 95 0.59
41 1 0.01
42 18 0.11
43 17 0.11
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12746 original size:82 final size:80
Alignment explanation
Indices: 12539--12762 Score: 299
Period size: 82 Copynumber: 2.8 Consensus size: 80
12529 AAACCAAGTA
* * * * *
12539 CCTTCGGGATTTAG-CCGGATATCGCAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
* *
12603 TAACTCGCACACATG
66 AAACTCGCACAAATG
* * * *
12618 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
12683 CAACTACTCGCACAAATG
66 -AA--ACTCGCACAAATG
*
12701 CCTTC-GGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
12763 CATCCGAATA
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 12 0.10
80 43 0.34
81 1 0.01
82 52 0.42
83 17 0.14
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
AAACTCGCACAAATG
Found at i:19657 original size:16 final size:17
Alignment explanation
Indices: 19630--19662 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
19620 ATTTCTAGAT
19630 TTTCGAAGATTTTTGGG
1 TTTCGAAGATTTTTGGG
19647 TTTCG-AGATTTTTGGG
1 TTTCGAAGATTTTTGGG
19663 GAGTTACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.15, C:0.06, G:0.30, T:0.48
Consensus pattern (17 bp):
TTTCGAAGATTTTTGGG
Found at i:22323 original size:46 final size:46
Alignment explanation
Indices: 22256--22424 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
22246 TAACCCGCCC
* * *
22256 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * *
22302 TAAGTGAACTCAGACTCAACTCAACGAGTTCGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCG--GAC--GTTCGCATCCA
* * *
22349 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
*
22394 TAAGTGAACTCGGACTCAACTCAACGA-TTCG
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCG
22425 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 14, Indels: 17
0.77 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 6 0.06
46 78 0.77
47 2 0.02
48 2 0.02
49 3 0.03
50 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:22368 original size:92 final size:91
Alignment explanation
Indices: 22261--22428 Score: 282
Period size: 92 Copynumber: 1.8 Consensus size: 91
22251 CGCCCTAAGT
* * *
22261 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
22326 CGAGTTCGATGCCTAGTTACATTTCAC
66 CGA-TTCGATGCCTAGTTACATTTCAC
* *
22353 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
22418 CGATTCGATGC
66 CGATTCGATGC
22429 TCAACCATCC
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
91 8 0.11
92 63 0.89
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (91 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGATTCGATGCCTAGTTACATTTCAC
Done.