Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1750
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: 27894
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:4589 original size:31 final size:31
Alignment explanation
Indices: 4551--4610 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
4541 AATAAATTTT
*
4551 ATAAAATTT-ATAAAATAATTTATTAAAAACC
1 ATAAAATTTAAAAAAATAATTTA-TAAAAACC
4582 ATAAAATTTAGAAAAAATAATTTATAAAA
1 ATAAAATTTA-AAAAAATAATTTATAAAA
4611 GTTTCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.35
32 5 0.19
33 12 0.46
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (31 bp):
ATAAAATTTAAAAAAATAATTTATAAAAACC
Found at i:4640 original size:52 final size:52
Alignment explanation
Indices: 4536--4656 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
4526 GAAATAATAA
4536 AAAAAAATAAATTTTATAAAATTTATAAAATAATTTATTAAAAACCATAAAA-TTT
1 AAAAAAAT-AA-TTTATAAAATTTATAAAATAA--TATTAAAAACCATAAAATTTT
* * *
4591 AGAAAAAATAATTTATAAAAGTTTCTAAAATGA-ATTAAAACCCATAAAATTTT
1 A-AAAAAATAATTTATAAAA-TTTATAAAATAATATTAAAAACCATAAAATTTT
*
4644 ATAAAAATAATTT
1 AAAAAAATAATTT
4657 TCTTTTTTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
52 26 0.44
53 4 0.07
54 9 0.15
55 13 0.22
56 7 0.12
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (52 bp):
AAAAAAATAATTTATAAAATTTATAAAATAATATTAAAAACCATAAAATTTT
Found at i:4826 original size:10 final size:10
Alignment explanation
Indices: 4811--4864 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
4801 AGAAAAATAA
4811 TTTATAAAAT
1 TTTATAAAAT
4821 TTTATAAAAT
1 TTTATAAAAT
4831 TTTA-AAATAT
1 TTTATAAA-AT
* * *
4841 TTAAT-TATT
1 TTTATAAAAT
4850 TTTATAAAAT
1 TTTATAAAAT
4860 TTTAT
1 TTTAT
4865 TTTTAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 8 0.23
10 27 0.77
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:4931 original size:17 final size:16
Alignment explanation
Indices: 4909--4940 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
4899 TTTTCTATTT
4909 TTTTTTTAATAAATTAA
1 TTTTTTT-ATAAATTAA
4926 TTTTTTTATAAATTA
1 TTTTTTTATAAATTA
4941 TATGGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTTATAAATTAA
Found at i:8046 original size:9 final size:9
Alignment explanation
Indices: 8003--8065 Score: 69
Period size: 9 Copynumber: 7.2 Consensus size: 9
7993 TTGGTTAAAA
*
8003 AATTAGCCG
1 AATTAACCG
*
8012 AATT-ACCC
1 AATTAACCG
*
8020 AATTACCCCG
1 AATTA-ACCG
8030 AA-TAACCG
1 AATTAACCG
8038 AATTAACCG
1 AATTAACCG
8047 AATTAACCG
1 AATTAACCG
8056 AATT-ACCG
1 AATTAACCG
8064 AA
1 AA
8066 AAATACCTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
8 17 0.37
9 25 0.54
10 4 0.09
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:8056 original size:26 final size:26
Alignment explanation
Indices: 8009--8065 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
7999 AAAAAATTAG
*
8009 CCGAATTACCCAATTACCCCGAATAA
1 CCGAATTACCCAATTACACCGAATAA
* *
8035 CCGAATTAACCGAATTA-ACCGAATTA
1 CCGAATT-ACCCAATTACACCGAATAA
8061 CCGAA
1 CCGAA
8066 AAATACCTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (26 bp):
CCGAATTACCCAATTACACCGAATAA
Found at i:25003 original size:12 final size:12
Alignment explanation
Indices: 24977--25015 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24967 CGTTTCTTCT
* *
24977 TTACTTACTTTC
1 TTACTTGCTTAC
*
24989 TTACTTGTTTAC
1 TTACTTGCTTAC
25001 TTACTTGCTTAC
1 TTACTTGCTTAC
25013 TTA
1 TTA
25016 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.56
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:25378 original size:50 final size:50
Alignment explanation
Indices: 25217--25396 Score: 157
Period size: 50 Copynumber: 3.6 Consensus size: 50
25207 GATAATAAAA
* * * ** * * * *
25217 TGCCAAAGCTATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGT-AC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
* * * ** *
25266 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTGTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
* * * * *
25316 TG-CATATACCATGTCACAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCA-ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
25366 TGCCAATGCCATGTCCCAGACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
25397 TTGGGATCTC
Statistics
Matches: 105, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
49 40 0.38
50 63 0.60
51 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
Found at i:27561 original size:40 final size:40
Alignment explanation
Indices: 27415--27598 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
27405 TTGAATGATG
* * * *
27415 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
27455 TCCGGACTAAGAT--CGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27494 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27533 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
27574 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27599 AACGAGTAGC
Statistics
Matches: 130, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
38 1 0.01
39 61 0.47
40 65 0.50
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27620 original size:79 final size:79
Alignment explanation
Indices: 27468--27621 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 79
27458 GGACTAAGAT
* **
27468 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAAA
27533 TCCGGGTTAAGTCC
66 TCCGGGTTAAGTCC
*
27547 CGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATTTGAACGAGTTA-CT
*
27610 ATATCC-GGTTAA
63 AAATCCGGGTTAA
27622 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
79 41 0.61
80 26 0.39
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (79 bp):
CGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAAA
TCCGGGTTAAGTCC
Done.