Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold782
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: 33009
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:6811 original size:40 final size:40
Alignment explanation
Indices: 6749--6933 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
6739 CCACTCGCAT
* * * * *
6749 AAAGCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATA
1 AAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACA
*
6789 AATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACA
1 AAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACA
* * *
6829 AATGCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACA
1 AAAGCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACA
* * * *
6870 AAAGCCTTC-GGATCTTAGTCCGGATGTAGCCGCTTGCACA
1 AAAGCCTTCGGGA-CTTAGCCCGGATATAGTCGCTAGCACA
6910 AAAGCCTTCGGGACTTAGCCCGGA
1 AAAGCCTTCGGGACTTAGCCCGGA
6934 GATCATTCGA
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 86 0.66
41 41 0.32
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (40 bp):
AAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACA
Found at i:6893 original size:81 final size:81
Alignment explanation
Indices: 6749--6933 Score: 214
Period size: 81 Copynumber: 2.3 Consensus size: 81
6739 CCACTCGCAT
* * * * * * *
6749 AAAGCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAATGCCTTCGGGACTTAGCCCGGA
1 AAAGCCTTCGGGACTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
*
6813 TATAGTCGCTAGCACA
66 TATAGCCGCTAGCACA
* * *
6829 AATGCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGCCTTC-GGATCTTAGTCCG
1 AAAGCCTTCGGGA-CTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGA-CTTAGCCCG
* *
6892 GATGTAGCCGCTTGCACA
64 GATATAGCCGCTAGCACA
6910 AAAGCCTTCGGGACTTAGCCCGGA
1 AAAGCCTTCGGGACTTAGCCCGGA
6934 GATCATTCGA
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
79 2 0.02
80 26 0.30
81 55 0.64
82 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (81 bp):
AAAGCCTTCGGGACTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
TATAGCCGCTAGCACA
Found at i:8165 original size:38 final size:38
Alignment explanation
Indices: 8123--8198 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
8113 CAAGAACTCC
*
8123 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCATTCCTTAGAATTTTCGGCCAAAAGAAATGAA
*
8161 TTCCTCATTCCTTAGAATTTTTGGCCAAAAGAAATGAA
1 TTCCTCATTCCTTAGAATTTTCGGCCAAAAGAAATGAA
8199 AAAGGATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (38 bp):
TTCCTCATTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:11580 original size:38 final size:38
Alignment explanation
Indices: 11515--11615 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
11505 ATTTGATGTG
* *
11515 TATCCGGGCTTAAAGACCCGCAGGCTTCCTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCACAGGCTTCCTGCTGGTAAAA
* * **
11555 TATCCGGGTTAAATCCCACAGGCTTCGTGTTGGTATTA
1 TATCCGGGTTAAATCCCACAGGCTTCCTGCTGGTAAAA
* *
11593 TATCAGGGATAAATCCCACAGGC
1 TATCCGGGTTAAATCCCACAGGC
11616 CTAGTGCTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 40 0.75
39 5 0.09
40 8 0.15
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCACAGGCTTCCTGCTGGTAAAA
Found at i:11627 original size:38 final size:38
Alignment explanation
Indices: 11544--11633 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
11534 GCAGGCTTCC
** * * * *
11544 TGCTGGTAAAATATCCGGGTTAAATCCCACAGGCTTCG
1 TGCTGGTATTATATCAGGGATAAATCCCACAGGCCTAG
*
11582 TGTTGGTATTATATCAGGGATAAATCCCACAGGCCTAG
1 TGCTGGTATTATATCAGGGATAAATCCCACAGGCCTAG
11620 TGCTGGTATTATAT
1 TGCTGGTATTATAT
11634 TCGGGCCTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (38 bp):
TGCTGGTATTATATCAGGGATAAATCCCACAGGCCTAG
Found at i:11679 original size:43 final size:43
Alignment explanation
Indices: 11631--11910 Score: 463
Period size: 43 Copynumber: 6.5 Consensus size: 43
11621 GCTGGTATTA
*
11631 TATTCGGGCCTTCGTACCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
11674 TATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
11717 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * * *
11760 TATTCAGGCCTTCGTGTCTAGTAGGCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
11803 TATTCGGGCCTTCATGCCTAGCAGGCTTCGTGCCGGTGATGTA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
11846 TATTCGGGCCTTCGTGCCTAGCAGGATTCGTGCCGGT-ATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
11888 TATTCGGGCCTTCGTGCCTAGCA
1 TATTCGGGCCTTCGTGCCTAGCA
11911 AGCGTAATAC
Statistics
Matches: 219, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
42 27 0.12
43 192 0.88
ACGTcount: A:0.12, C:0.25, G:0.32, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:20045 original size:85 final size:85
Alignment explanation
Indices: 19926--20081 Score: 197
Period size: 85 Copynumber: 1.8 Consensus size: 85
19916 CATCCATTAT
* *
19926 GAACTTAGACCACTCAACGAGCTCGAATGATCACATCCATAATGAACTCAAACC-TCTCAACGAG
1 GAACTTAGACCACTCAACAAGCTCGAATGATCACATACATAATGAACTCAAACCGT-TCAACGAG
*
19990 CTTGGATGCCACATAGATCAC
65 CTCGGATGCCACATAGATCAC
* * ** * * **
20011 GAACTTGGACCACTCAACAAGTTCGAATTCTCACATATATCATGAACTCGGACCGTTCAACGAGC
1 GAACTTAGACCACTCAACAAGCTCGAATGATCACATACATAATGAACTCAAACCGTTCAACGAGC
20076 TCGGAT
66 TCGGAT
20082 TTCTAAATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
85 58 0.98
86 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (85 bp):
GAACTTAGACCACTCAACAAGCTCGAATGATCACATACATAATGAACTCAAACCGTTCAACGAGC
TCGGATGCCACATAGATCAC
Found at i:23926 original size:46 final size:46
Alignment explanation
Indices: 23876--24000 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 46
23866 TTTTGCATCC
* *
23876 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-ATG-TCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA--GATGCAACAGGATCA
* *
23922 GAACTCGTTGAGTTGAGTCCGAGTTCA-TGAGATGTAACTAGGCATCA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAAC-AGG-ATCA
*
23969 GAACTCGTTGAGTTGAGTCTGAGTTCACTTAG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAG
24001 GGGCGGGTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
43 6 0.09
45 4 0.06
46 27 0.40
47 28 0.41
48 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAACAGGATCA
Found at i:31359 original size:46 final size:46
Alignment explanation
Indices: 31309--31479 Score: 213
Period size: 46 Copynumber: 3.7 Consensus size: 46
31299 TGGTTGAGCA
*
31309 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * ** *
31355 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGA--GATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
*
31400 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
31446 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
31480 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
44 2 0.02
45 34 0.33
46 66 0.63
47 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:31461 original size:91 final size:91
Alignment explanation
Indices: 31306--31474 Score: 302
Period size: 91 Copynumber: 1.9 Consensus size: 91
31296 GGATGGTTGA
* *
31306 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
31371 TGAGTCCGAGTTCGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGATGTAACTAG
* *
31397 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
31462 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
31475 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGATGTAACTAG
Done.