Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold443
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: 237995
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 18295 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:230993 original size:95 final size:96
Alignment explanation
Indices: 230877--231062 Score: 365
Period size: 95 Copynumber: 1.9 Consensus size: 96
230867 TTCTTCAATT
230877 CTTAAACATTAACAAACAACGTATGCAAACATGAAACACCATATACATAAAAGACTCGTTACTAC
1 CTTAAACATTAACAAACAACGTATGCAAACATGAAACACCATATACATAAAAGACTCGTTACTAC
230942 AAATGACTATAAAATTGATAATTTATATAAC
66 AAATGACTATAAAATTGATAATTTATATAAC
230973 CTTAAACATT-ACAAACAACGTATGCAAACATGAAACACCATATACATAAAAGACTCGTTACTAC
1 CTTAAACATTAACAAACAACGTATGCAAACATGAAACACCATATACATAAAAGACTCGTTACTAC
231037 AAATGACTATAAAATTGATAATTTAT
66 AAATGACTATAAAATTGATAATTTAT
231063 TANNNNNNNN
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 80 0.89
96 10 0.11
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (96 bp):
CTTAAACATTAACAAACAACGTATGCAAACATGAAACACCATATACATAAAAGACTCGTTACTAC
AAATGACTATAAAATTGATAATTTATATAAC
Found at i:232974 original size:24 final size:24
Alignment explanation
Indices: 232919--232974 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
232909 GAATTATAAA
*
232919 ATATAT-AAAATATGTACATATCT
1 ATATATAAAAATATGTACATATAT
* *
232942 ATATGTAAAAATATGTATATATAT
1 ATATATAAAAATATGTACATATAT
*
232966 ATTTATAAA
1 ATATATAAA
232975 GGTTAGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (24 bp):
ATATATAAAAATATGTACATATAT
Found at i:233979 original size:5 final size:5
Alignment explanation
Indices: 233964--233996 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
233954 TTCGTTTAAG
233964 AAATCA AAATA AAATA AAATA AAATA AAATA AA
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AA
233997 TACAACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:234914 original size:88 final size:88
Alignment explanation
Indices: 234843--235353 Score: 631
Period size: 88 Copynumber: 5.8 Consensus size: 88
234833 TCTTTGATCT
* *
234843 GCTCCA-CTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGAAGGAA
1 GCTCCATC-ACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
*
234907 GGCAAGATCTGTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * *
234931 GCTCCATCACAACTGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
* *
234996 GCAAGATCTATTGTCTTCGACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * *
235019 GCTCCATCACAACCGAGAGAGGCAAGGTTTGCGTCTTCGACCTACTTCGCTGTCAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
*
235084 GCAAGATTTTTTGTCTTCAACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * * *
235107 GCTCCATCACAACCGAGAGAGGAAAGGTTTGTGTCTTTGATCTGCTTCGTTGTTAATGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
*
235172 GCAAGATCTTTTGTCTTTAACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * *
235195 GCTCCA-CTGCAACCAATGA-AGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 GCTCCATC-ACAACCGA-GAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* ** *
235257 GGGCAAGATCTGCT-TCTTTAACCA
64 AGGCAAGATCTTTTGTCTTCAACCA
* ** * * * *
235281 GCTCCACCGTAACCAATGA-AGGCAAGGCTT-TGTTTTCGATCTGCTTCGTTGTTAATGCAGGAA
1 GCTCCATCACAACCGA-GAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
235344 GGCAAGATCT
65 GGCAAGATCT
235354 GCTTCTTTAA
Statistics
Matches: 384, Mismatches: 35, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
86 78 0.20
87 42 0.11
88 261 0.68
89 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (88 bp):
GCTCCATCACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAG
GCAAGATCTTTTGTCTTCAACCA
Found at i:234954 original size:44 final size:44
Alignment explanation
Indices: 234906--235143 Score: 163
Period size: 44 Copynumber: 5.4 Consensus size: 44
234896 CAATGAAGGA
* *
234906 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACTGAGAG
1 AGGCAAGATTTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
* * **
234950 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGC-TGTCAA-TGCAG-G
1 AGGCAAGATTTGTTGTCTTCGACCAGC-TC-CATCACAACTG-AGAG
* * *
234993 AAGGCAAGATCTATTGTCTTCGACCAGCTCCATCACAACCGAGAG
1 -AGGCAAGATTTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
* * **
235038 AGGCAAGGTTTG-CGTCTTCGACCTA-CTTCGC-TGTCAA-TGCAG-G
1 AGGCAAGATTTGTTGTCTTCGACC-AGC-TC-CATCACAACTG-AGAG
* * *
235081 AAGGCAAGATTTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 -AGGCAAGATTTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
* *
235126 AGGAAAGGTTTG-TGTCTT
1 AGGCAAGATTTGTTGTCTT
235144 TGATCTGCTT
Statistics
Matches: 146, Mismatches: 30, Indels: 37
0.69 0.14 0.17
Matches are distributed among these distances:
43 36 0.25
44 81 0.55
45 29 0.20
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (44 bp):
AGGCAAGATTTGTTGTCTTCGACCAGCTCCATCACAACTGAGAG
Found at i:236615 original size:21 final size:21
Alignment explanation
Indices: 236591--236659 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
236581 TTAGCCTCTC
236591 CATTTTTACTT-TTTCATTTTT
1 CATTTTT-CTTCTTTCATTTTT
*
236612 CATTTTT-TTCATTCATTTTTT
1 CATTTTTCTTCTTTCA-TTTTT
*
236633 CATTTTTCTTCTTT-TTTTTT
1 CATTTTTCTTCTTTCATTTTT
236653 CATTTTT
1 CATTTTT
236660 TGTTTGAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.05
20 16 0.38
21 19 0.45
22 5 0.12
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (21 bp):
CATTTTTCTTCTTTCATTTTT
Found at i:236626 original size:20 final size:19
Alignment explanation
Indices: 236603--236660 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
236593 TTTTTACTTT
236603 TTCATTTTTCATTTTTTTC
1 TTCATTTTTCATTTTTTTC
236622 ATTCATTTTTTCATTTTTCTTC
1 -TTCA-TTTTTCATTTTT-TTC
**
236644 TTTTTTTTTCATTTTTT
1 TTCATTTTTCATTTTTT
236661 GTTTGAGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.03
20 16 0.47
21 14 0.41
22 3 0.09
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (19 bp):
TTCATTTTTCATTTTTTTC
Found at i:236631 original size:28 final size:28
Alignment explanation
Indices: 236600--236660 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
236590 CCATTTTTAC
236600 TTTTTCATTTTTCATT-TTTTTCATTCAT
1 TTTTTCATTTTTC-TTCTTTTTCATTCAT
**
236628 TTTTTCATTTTTCTTCTTTTTTTTTCAT
1 TTTTTCATTTTTCTTCTTTTTCATTCAT
236656 TTTTT
1 TTTTT
236661 GTTTGAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTCATTTTTCTTCTTTTTCATTCAT
Found at i:237514 original size:28 final size:28
Alignment explanation
Indices: 237483--237551 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
237473 TCTTTCTTTT
237483 TTTTCTTATTTTGACTTTGATT-TTTTGA
1 TTTT-TTATTTTGACTTTGATTATTTTGA
* **
237511 TTTTTTATTTTGATTTTTTTTATTTTGA
1 TTTTTTATTTTGACTTTGATTATTTTGA
237539 TTTTTTATTTTGA
1 TTTTTTATTTTGA
237552 GTCGAAACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 14 0.38
28 23 0.62
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (28 bp):
TTTTTTATTTTGACTTTGATTATTTTGA
Found at i:237521 original size:13 final size:14
Alignment explanation
Indices: 237482--237551 Score: 74
Period size: 13 Copynumber: 5.0 Consensus size: 14
237472 TTCTTTCTTT
237482 TTTTTCTTATTTTGA
1 TTTTT-TTATTTTGA
**
237497 CTTTGATT-TTTTGA
1 -TTTTTTTATTTTGA
237511 -TTTTTTATTTTGA
1 TTTTTTTATTTTGA
237524 TTTTTTTTATTTTGA
1 -TTTTTTTATTTTGA
237539 -TTTTTTATTTTGA
1 TTTTTTTATTTTGA
237552 GTCGAAACTC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.09
13 19 0.40
14 6 0.13
15 15 0.32
16 3 0.06
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTTTTTATTTTGA
Found at i:237529 original size:15 final size:15
Alignment explanation
Indices: 237481--237544 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
237471 TTTCTTTCTT
237481 TTTTTTCTTATTTTGA
1 TTTTTT-TTATTTTGA
* **
237497 CTTTGATT-TTTTGA
1 TTTTTTTTATTTTGA
237511 --TTTTTTATTTTGA
1 TTTTTTTTATTTTGA
237524 TTTTTTTTATTTTGA
1 TTTTTTTTATTTTGA
237539 TTTTTT
1 TTTTTT
237545 ATTTTGAGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
14 6 0.15
15 21 0.52
16 3 0.08
ACGTcount: A:0.12, C:0.03, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTTTTTATTTTGA
Found at i:237541 original size:21 final size:22
Alignment explanation
Indices: 237481--237542 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
237471 TTTCTTTCTT
* *
237481 TTTTTTCTTATTTTGACTTTGA
1 TTTTTTATTATTTTGATTTTGA
237503 TTTTTTGATT-TTTT-ATTTTGA
1 TTTTTT-ATTATTTTGATTTTGA
237524 TTTTTT-TTATTTTGATTTT
1 TTTTTTATTATTTTGATTTT
237543 TTATTTTGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 4 0.11
21 17 0.49
22 10 0.29
23 2 0.06
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTTATTATTTTGATTTTGA
Found at i:237549 original size:21 final size:21
Alignment explanation
Indices: 237482--237549 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
237472 TTCTTTCTTT
*
237482 TTTTTCTTATTTTGA-CTTTGA
1 TTTTT-TTATTTTGATTTTTGA
* *
237503 TTTTTTGATTTT-TTATTTTGA
1 TTTTTTTATTTTGAT-TTTTGA
*
237524 TTTTTTTTATTTTGATTTTTTA
1 -TTTTTTTATTTTGATTTTTGA
237546 TTTT
1 TTTT
237550 GAGTCGAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 6 0.16
21 14 0.38
22 16 0.43
23 1 0.03
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTTTTATTTTGATTTTTGA
Done.