Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3604
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: 33089
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:973 original size:22 final size:22
Alignment explanation
Indices: 948--993 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
938 TTTATCAAAA
948 TATT-TTTTATA-TT-AATATT
1 TATTATTTTATATTTAAATATT
967 TATTATTTTATATTTAAATATT
1 TATTATTTTATATTTAAATATT
989 TATTA
1 TATTA
994 AACATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 2 0.08
22 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATTTTATATTTAAATATT
Found at i:1810 original size:104 final size:104
Alignment explanation
Indices: 1688--1911 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
1678 AATGGATATC
1688 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
1753 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
1792 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
1857 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
1896 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
1912 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:2273 original size:29 final size:29
Alignment explanation
Indices: 2240--2303 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
2230 TAATCCACCA
2240 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
2269 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
2299 CCCAA
1 CCCAA
2304 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:2277 original size:30 final size:30
Alignment explanation
Indices: 2247--2303 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2237 CCACCCAACT
2247 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
2276 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
2304 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:9364 original size:104 final size:104
Alignment explanation
Indices: 9242--9465 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
9232 AATGGATATC
9242 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
9307 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
9346 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
9411 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
9450 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
9466 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:9827 original size:29 final size:29
Alignment explanation
Indices: 9794--9857 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
9784 TAATCCACCA
9794 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
9823 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
9853 CCCAA
1 CCCAA
9858 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:9831 original size:30 final size:30
Alignment explanation
Indices: 9801--9857 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9791 CCACCCAACT
9801 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
9830 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
9858 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:14890 original size:24 final size:24
Alignment explanation
Indices: 14825--14970 Score: 233
Period size: 24 Copynumber: 6.1 Consensus size: 24
14815 GCCTAGCCTC
14825 TTTAATAACTGGGGCA-AAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
14848 TTTAATAA-TAGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
14871 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
* *
14895 TTTAACAACTGGGGCATAAACCCTT
1 TTTAATAACTGGGGCATAAGCCC-T
*
14920 TTTAATAACTAGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
14944 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
14968 TTT
1 TTT
14971 GCACTTCCTC
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
22 6 0.05
23 23 0.21
24 62 0.55
25 21 0.19
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (24 bp):
TTTAATAACTGGGGCATAAGCCCT
Found at i:14935 original size:49 final size:49
Alignment explanation
Indices: 14825--14970 Score: 235
Period size: 49 Copynumber: 3.0 Consensus size: 49
14815 GCCTAGCCTC
*
14825 TTTAATAACTGGGGCA-AAGCCCTTTTAATAA-TAGGGCATAAGCCC-T
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
* *
14871 TTTAATAACTGGGGCATAAGCCCTTTTAACAACTGGGGCATAAACCCTT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
*
14920 TTTAATAACTAGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
14969 TT
1 TT
14971 GCACTTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
46 16 0.18
47 14 0.15
48 12 0.13
49 49 0.54
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (49 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
Found at i:14943 original size:73 final size:70
Alignment explanation
Indices: 14825--14970 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 70
14815 GCCTAGCCTC
* *
14825 TTTAATAACTGGGGCAAAGCCCTTTTAATAATAGGGCATAAGCCCTTTTAATAACTGGGGCATAA
1 TTTAACAACTGGGGCAAAACCCTTTTAATAATAGGGCATAAGCCCTTTTAATAACTGGGGCATAA
14890 GCCCT
66 GCCCT
14895 TTTAACAACTGGGGCATAAACCCTTTTTAATAACTAGGGCATAAGCCCTTTTAATAACTGGGGCA
1 TTTAACAACTGGGGCA-AAACCC-TTTTAATAA-TAGGGCATAAGCCCTTTTAATAACTGGGGCA
14960 TAAGCCCT
63 TAAGCCCT
14968 TTT
1 TTT
14971 GCACTTCCTC
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 15 0.21
71 5 0.07
72 9 0.13
73 42 0.59
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (70 bp):
TTTAACAACTGGGGCAAAACCCTTTTAATAATAGGGCATAAGCCCTTTTAATAACTGGGGCATAA
GCCCT
Found at i:15044 original size:20 final size:20
Alignment explanation
Indices: 15019--15085 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
15009 TTATGAATAC
*
15019 ATCATGTGCATATCATATAT
1 ATCATGTGCATATCATACAT
*
15039 ATCATGCGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
15059 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
15079 ACCATGT
1 ATCATGT
15086 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:16951 original size:31 final size:31
Alignment explanation
Indices: 16916--16979 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
16906 CCTTTTCATG
* *
16916 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCAAAGCCT
**
16947 TTTCATATTTCATATTACTAGGCCAAAGCCT
1 TTTCATATTTCATAACACTAGGCCAAAGCCT
16978 TT
1 TT
16980 ACTGTAGACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCAAAGCCT
Found at i:17284 original size:26 final size:25
Alignment explanation
Indices: 17188--17285 Score: 119
Period size: 25 Copynumber: 3.9 Consensus size: 25
17178 CTGGACGCCT
* *
17188 AGCCTCTTTTAAT-AACTAGGGCAAA
1 AGCC-CTTTTGATAAACTGGGGCAAA
17213 A-CCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
17237 AGCCATTTTAATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
17262 AGCCCTTTTCGGTAAACTGGGGCA
1 AGCCCTTTT-GATAAACTGGGGCA
17286 TAACCATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
23 7 0.11
24 14 0.22
25 30 0.48
26 12 0.19
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:17366 original size:20 final size:20
Alignment explanation
Indices: 17343--17389 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
17333 TTATGAATAC
17343 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
17362 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
17383 ATCATGT
1 ATCATGT
17390 ATATCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:31780 original size:40 final size:40
Alignment explanation
Indices: 31735--31834 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
31725 ATGATGATTT
* *
31735 GGCTATATATGGCACTTAGTGTACGACTCGAGATAGCTTC
1 GGCTATATATGGCACTTAGTGTACGACTCAAAATAGCTTC
* * * *
31775 GGCTATATATGGCACTTAGTTTGCGATTCAAAATAGCTTT
1 GGCTATATATGGCACTTAGTGTACGACTCAAAATAGCTTC
*
31815 GGCTATATGTGGCACTTAGT
1 GGCTATATATGGCACTTAGT
31835 ATGAGAGACT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
GGCTATATATGGCACTTAGTGTACGACTCAAAATAGCTTC
Done.