Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2391
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: 56218
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3114 original size:48 final size:48
Alignment explanation
Indices: 2970--3247 Score: 336
Period size: 48 Copynumber: 5.9 Consensus size: 48
2960 CACGTAGTAA
* * *
2970 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACAGATT
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * * * *
3018 GAAG-C--TG--ATAGCCCAG-CTATGGTCTTACACGATG-TCTCATATC
1 GATGCCAATGCCATATCCCAGAC-ATGGTCTTACATG-GGATCACATATC
*
3061 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATACC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* ** * * *
3109 AATGCCAATGCCATCGCCCAAACATGGTTTTACATGGGATCACATATT
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
*
3157 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
*
3205 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCAC
3248 TCATAACCCT
Statistics
Matches: 194, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
43 29 0.15
44 2 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 156 0.80
49 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:13302 original size:39 final size:39
Alignment explanation
Indices: 13257--13414 Score: 149
Period size: 39 Copynumber: 3.7 Consensus size: 39
13247 TGGTTGAGCA
13257 TCCGAACTCGTTGAGTTGAGTCCGAGTTCTGGATGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCTGGATGAATG
13296 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCTG-GATG-AA-T--G
*
13338 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTT--C---TGGAT--GAATG
* *
13386 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
13415 ACTTAGGGGC
Statistics
Matches: 100, Mismatches: 3, Indels: 27
0.77 0.02 0.21
Matches are distributed among these distances:
38 2 0.02
39 33 0.33
40 1 0.01
42 1 0.01
44 29 0.29
46 27 0.27
48 1 0.01
49 2 0.02
50 1 0.01
51 2 0.02
52 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (39 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCTGGATGAATG
Found at i:13344 original size:44 final size:41
Alignment explanation
Indices: 13254--13368 Score: 157
Period size: 39 Copynumber: 2.8 Consensus size: 41
13244 GGATGGTTGA
13254 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCTGGATGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCTGGATGAAT
13295 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GTAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCTG-GATG-AA-T
13335 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
13369 ACTTATGGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
38 2 0.03
39 33 0.49
40 1 0.01
41 1 0.01
42 1 0.01
44 29 0.43
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (41 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCTGGATGAAT
Found at i:15374 original size:28 final size:31
Alignment explanation
Indices: 15342--15401 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
15332 GATTCGGCCA
15342 TGGGAGAAA-T-G-AGGGGATAGATTGTTGT
1 TGGGAGAAATTGGAAGGGGATAGATTGTTGT
15370 TGGGAGAAATTGGAAGGGGATAGATTGTTGT
1 TGGGAGAAATTGGAAGGGGATAGATTGTTGT
15401 T
1 T
15402 CTTTGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 9 0.31
29 1 0.03
30 1 0.03
31 18 0.62
ACGTcount: A:0.28, C:0.00, G:0.42, T:0.30
Consensus pattern (31 bp):
TGGGAGAAATTGGAAGGGGATAGATTGTTGT
Found at i:31577 original size:48 final size:48
Alignment explanation
Indices: 31506--31783 Score: 340
Period size: 48 Copynumber: 5.9 Consensus size: 48
31496 AGGGTTATGA
31506 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
*
31554 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
* * *
31602 GTGATCCCATGTAAAACCATGTTTGGG-CAATGGCATTGGCATCGGTAT
1 GTGATCCCATGTAAGACCATGTCTGGGAC-ATGGCATTGGCATCGATAT
*
31650 GTGATCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
* * * * * *
31698 GAGA-CATCGTGTAAGACCATAG-CTGGG-CTAT--CA---GCTTCAATCT
1 GTGATC-CCATGTAAGACCAT-GTCTGGGAC-ATGGCATTGGCATCGATAT
* *
31741 GTGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
31784 TTACTACGTG
Statistics
Matches: 195, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
43 29 0.15
44 1 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 158 0.81
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (48 bp):
GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
Found at i:35294 original size:43 final size:43
Alignment explanation
Indices: 35233--35421 Score: 283
Period size: 43 Copynumber: 4.4 Consensus size: 43
35223 ACATATCATT
* *
35233 TCACCGGCATTACGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
35276 TCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
35319 TCACCGGCACTAATCCTGCTAGGCACAAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
35362 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
35404 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
35422 GGGATTTATC
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 15 0.11
42 2 0.02
43 116 0.87
ACGTcount: A:0.30, C:0.34, G:0.22, T:0.13
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:35447 original size:38 final size:38
Alignment explanation
Indices: 35393--35476 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
35383 GGCACGAAGG
* * *
35393 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
35431 CCCGGATATAATACCAGCACGAAGCCTGTGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
35469 CCCGAATA
1 CCCGAATA
35477 CACATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:47853 original size:15 final size:16
Alignment explanation
Indices: 47829--47861 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
47819 AAGTTGTCTC
*
47829 ATAAACAATT-CATAT
1 ATAAAAAATTCCATAT
47844 ATAAAAAATTCCATAT
1 ATAAAAAATTCCATAT
47860 AT
1 AT
47862 TACATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAAATTCCATAT
Done.