Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2612
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: 42900
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9612 original size:19 final size:19
Alignment explanation
Indices: 9588--9627 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
9578 AGTAGCCGCT
9588 TAGACTCTATAGTGTACGC
1 TAGACTCTATAGTGTACGC
*
9607 TAGACTCTTTAGTGTACGC
1 TAGACTCTATAGTGTACGC
9626 TA
1 TA
9628 TCTATCACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (19 bp):
TAGACTCTATAGTGTACGC
Found at i:12020 original size:16 final size:18
Alignment explanation
Indices: 11989--12023 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
11979 TATATATCTT
11989 TATATCTTATTATATATA
1 TATATCTTATTATATATA
12007 TATATCTTATTATATAT
1 TATATCTTATTATATAT
12024 GTGCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATCTTATTATATATA
Found at i:12150 original size:36 final size:37
Alignment explanation
Indices: 12064--12170 Score: 105
Period size: 36 Copynumber: 2.9 Consensus size: 37
12054 ATTTTTTAGC
12064 TTATATATATACATACATACATATTTTTATATACTTT
1 TTATATATATACATACATACATATTTTTATATACTTT
* * *
12101 ATA-AT-TCTAACATACGTACATATTTTT-TA-ACTTAT
1 TTATATATAT-ACATACATACATATTTTTATATACTT-T
* **
12136 TTATATATATACATACTTATGTATTATTTATATAC
1 TTATATATATACATACATACATATT-TTTATATAC
12171 CACACATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
34 4 0.07
35 7 0.13
36 33 0.60
37 7 0.13
38 2 0.04
39 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (37 bp):
TTATATATATACATACATACATATTTTTATATACTTT
Found at i:20055 original size:15 final size:15
Alignment explanation
Indices: 20035--20066 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20025 TATACAAGAA
20035 AAATATAAAAGACAT
1 AAATATAAAAGACAT
*
20050 AAATATAAAATACAT
1 AAATATAAAAGACAT
20065 AA
1 AA
20067 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:27010 original size:11 final size:11
Alignment explanation
Indices: 26990--27047 Score: 89
Period size: 11 Copynumber: 5.1 Consensus size: 11
26980 TAGTAGTTTC
26990 TTCAAAAAAAA
1 TTCAAAAAAAA
*
27001 TTTGAAAAAAAA
1 -TTCAAAAAAAA
27013 TTCGAAAAAAAA
1 TTC-AAAAAAAA
27025 TTCAAAAAAAA
1 TTCAAAAAAAA
27036 TTCAAAAAAAA
1 TTCAAAAAAAA
27047 T
1 T
27048 GGTTTCCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
11 22 0.51
12 21 0.49
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:27031 original size:23 final size:22
Alignment explanation
Indices: 26990--27047 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 22
26980 TAGTAGTTTC
*
26990 TTCAAAAAAAATTTGAAAAAAAA
1 TTCAAAAAAAA-TTCAAAAAAAA
27013 TTCGAAAAAAAATTCAAAAAAAA
1 TTC-AAAAAAAATTCAAAAAAAA
27036 TTCAAAAAAAAT
1 TTCAAAAAAAAT
27048 GGTTTCCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 9 0.27
23 16 0.48
24 8 0.24
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (22 bp):
TTCAAAAAAAATTCAAAAAAAA
Found at i:27108 original size:16 final size:16
Alignment explanation
Indices: 27087--27124 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
27077 ATCAAGTTGG
27087 AAAAAAAATTTCGTGA
1 AAAAAAAATTTCGTGA
*
27103 AAAAAAAATTTTGTGA
1 AAAAAAAATTTCGTGA
27119 AAAAAA
1 AAAAAA
27125 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.24
Consensus pattern (16 bp):
AAAAAAAATTTCGTGA
Found at i:33823 original size:40 final size:40
Alignment explanation
Indices: 33592--33823 Score: 251
Period size: 40 Copynumber: 5.8 Consensus size: 40
33582 TTGAATGATG
* * * * *
33592 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGA-GTTACTAAA
*
33632 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
*
33672 TCCGGACTAAGAT-CCGAAGGCATTTGTGA-GAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGT-ACGAGTTACTAAA
* *
33712 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
* *
33752 TCCGGGTTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* * *
33792 -CCGGGCTATGTCCCGAAGACATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
33824 AGCTATATCC
Statistics
Matches: 171, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
39 35 0.20
40 127 0.74
41 9 0.05
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:40653 original size:47 final size:47
Alignment explanation
Indices: 40581--40693 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
40571 CAGCACATAT
** *
40581 TGGACAAGCCACCAATTTTGCAGACAAGCTGCCAATACGCATAGTTG
1 TGGACAAGCCACCAAAATTGCAGACAAGCTGCCAATACACATAGTTG
* * * *
40628 TGGACAAGCCACTAAAATTGTAGACAAGCTGCCAATGCATATAGTTG
1 TGGACAAGCCACCAAAATTGCAGACAAGCTGCCAATACACATAGTTG
*
40675 TGGTCAAGCCACCAAAATT
1 TGGACAAGCCACCAAAATT
40694 TGCAAATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (47 bp):
TGGACAAGCCACCAAAATTGCAGACAAGCTGCCAATACACATAGTTG
Found at i:40883 original size:15 final size:15
Alignment explanation
Indices: 40863--40897 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40853 AACAAATAGC
40863 CATGATAGTACACAA
1 CATGATAGTACACAA
*
40878 CATGATATTACACAA
1 CATGATAGTACACAA
40893 CATGA
1 CATGA
40898 GATTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (15 bp):
CATGATAGTACACAA
Found at i:40902 original size:15 final size:15
Alignment explanation
Indices: 40871--40902 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40861 GCCATGATAG
*
40871 TACACAACATGATAT
1 TACACAACATGAGAT
40886 TACACAACATGAGAT
1 TACACAACATGAGAT
40901 TA
1 TA
40903 GAAAATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (15 bp):
TACACAACATGAGAT
Done.