Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1808
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: 43518
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4480 original size:27 final size:27
Alignment explanation
Indices: 4450--4501 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
4440 TCATGTGAAA
* *
4450 TTGAATGGAAAATTATTGTTACATGAT
1 TTGAATGGAAAATTACTATTACATGAT
**
4477 TTGAATGTTAAATTACTATTACATG
1 TTGAATGGAAAATTACTATTACATG
4502 GGTTGTATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (27 bp):
TTGAATGGAAAATTACTATTACATGAT
Found at i:7929 original size:55 final size:53
Alignment explanation
Indices: 7814--7939 Score: 132
Period size: 55 Copynumber: 2.3 Consensus size: 53
7804 GAAAAATAAA
*
7814 AAAATTTATTAATAAAAATAAAATATAGATTAACAATTTTATATTATATAATACT
1 AAAATTTATTAATAAAAATAAAATATAGA-TAACAA-TTTATATTAAATAATACT
*
7869 TAAATTTATTAAATAAAATATTAAAATGATAGA-AAC-A-TTATATTAAATAATAACT
1 AAAATTTATT-AATAAAA-A-TAAAAT-ATAGATAACAATTTATATTAAATAAT-ACT
*
7924 AAAATTATATTTATAA
1 AAAATT-TATTAATAA
7940 TAATTATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
54 13 0.21
55 21 0.34
56 12 0.20
57 4 0.07
58 6 0.10
59 5 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (53 bp):
AAAATTTATTAATAAAAATAAAATATAGATAACAATTTATATTAAATAATACT
Found at i:10474 original size:14 final size:15
Alignment explanation
Indices: 10455--10484 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
10445 AACATGCATA
10455 AAATAACC-AATTTC
1 AAATAACCAAATTTC
10469 AAATAACCAAATTTC
1 AAATAACCAAATTTC
10484 A
1 A
10485 TTCAACCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAACCAAATTTC
Found at i:11188 original size:20 final size:20
Alignment explanation
Indices: 11164--11213 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
11154 TGAACCACTC
*
11164 CATTTACTTTCTTACCA-TT
1 CATTTACTTACTTACCATTT
*
11183 CTATTTACTTACTTTCCATTT
1 C-ATTTACTTACTTACCATTT
11204 CATTTACTTA
1 CATTTACTTA
11214 GCTTTAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 23 0.85
21 3 0.11
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (20 bp):
CATTTACTTACTTACCATTT
Found at i:13522 original size:25 final size:25
Alignment explanation
Indices: 13440--13523 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 25
13430 AGGTAACCTA
* * *
13440 CCACAAAGGCTTCCCAAATAAATTG
1 CCACAAAGGCTTCCCAAGTGACTTG
** * **
13465 CCACAAAGGCTTTACAGGTGACTCA
1 CCACAAAGGCTTCCCAAGTGACTTG
*
13490 CCAGAAAGGCTTCCCAAGTGACTTG
1 CCACAAAGGCTTCCCAAGTGACTTG
*
13515 CCATAAAGG
1 CCACAAAGG
13524 TTTGGTTTGG
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (25 bp):
CCACAAAGGCTTCCCAAGTGACTTG
Found at i:23034 original size:19 final size:18
Alignment explanation
Indices: 23002--23042 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
22992 AATTCGAAAC
*
23002 AAAATAGAAGATTTTAGA
1 AAAATAGAAAATTTTAGA
*
23020 AAAATTAGAAAATTTTGGA
1 AAAA-TAGAAAATTTTAGA
23039 AAAA
1 AAAA
23043 GGAGTCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.27
Consensus pattern (18 bp):
AAAATAGAAAATTTTAGA
Found at i:26172 original size:39 final size:40
Alignment explanation
Indices: 26073--26212 Score: 162
Period size: 39 Copynumber: 3.5 Consensus size: 40
26063 CTCGAATGAT
*
26073 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACTAC
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACTAC
*
26114 ATCCGGACTAAGAT--C-AAGGCATTTGTGCTAGCGACTA-
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACTAC
* * * *
26151 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACTAC
* *
26191 ATCCGGGTTAAGACCCGAAGGC
1 ATCCGGGCTAAGTCCCGAAGGC
26213 CTTGTGCGAG
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
36 1 0.01
37 11 0.13
38 9 0.10
39 32 0.37
40 21 0.24
41 11 0.13
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACTAC
Found at i:26218 original size:78 final size:78
Alignment explanation
Indices: 26073--26219 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 78
26063 CTCGAATGAT
* * * * *
26073 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACTACATCCGGACTAAGATCAAGGCATTT
1 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGCGACCACATCCGGACTAAGACCAAGGCACTT
26138 GTGCTAGCGACTA
66 GTGCTAGCGACTA
* * **
26151 ATCCGGGCTAAGTCCCGAAGGCATTTATGCT-AGTGACCATATCCGGGTTAAGACCCGAAGGC-C
1 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGCGACCACATCCGGACTAAGA-CC-AAGGCAC
26214 TTGTGC
64 TTGTGC
26220 GAGTGGTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
77 17 0.29
78 36 0.62
79 5 0.09
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (78 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGCGACCACATCCGGACTAAGACCAAGGCACTT
GTGCTAGCGACTA
Found at i:34190 original size:40 final size:40
Alignment explanation
Indices: 34096--34240 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
34086 TACTCGAATG
*
34096 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
34137 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
34177 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
34217 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
34241 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:37038 original size:41 final size:40
Alignment explanation
Indices: 36978--37108 Score: 117
Period size: 41 Copynumber: 3.3 Consensus size: 40
36968 TCGCACAAGG
* * *
36978 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGC
* * *
37018 CTTCGGGACTTTAGCCCGGATTTAGTCGCTAGCACAAATGC
1 CTTCGGGAC-TTAACCCGGATATAGTCACTAGCACAAATGC
** * *
37059 CTTC-GGATCTT-GTCCGGATATAGTCGCTTAGCA-AAAAGC
1 CTTCGGGA-CTTAACCCGGATATAGTCAC-TAGCACAAATGC
37098 CTTC-GGACTTA
1 CTTCGGGACTTA
37109 GCGACTTCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.04
39 26 0.33
40 18 0.23
41 31 0.40
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (40 bp):
CTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGC
Done.