Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1854
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: 19853
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Found at i:6993 original size:44 final size:41
Alignment explanation
Indices: 6848--7014 Score: 112
Period size: 42 Copynumber: 4.0 Consensus size: 41
6838 TCCTCGTTCA
* * * *
6848 AATGCCTTCG-GGACATTAGGCCCGG-TATAGTAACTACGCACA
1 AATGCCTTCGCGGACTTTA-ACCCGGATTTAGTAACT-CGC-CC
*
6890 AATGTCTTCG-GGCAC-TTAACCCGGATTTAGTAACTCGCCC
1 AATGCCTTCGCGG-ACTTTAACCCGGATTTAGTAACTCGCCC
6930 AATGCCTTCGCGGATCTTTAACCCGGTATTTTAGGT-ACTCGTCACC
1 AATGCCTTCGCGGA-CTTTAACCCGG-A-TTTA-GTAACTCG-C-CC
* * * *
6976 AATGCCTTCGTGG-CTTTAGCCCGGAATATAGTATCTCGC
1 AATGCCTTCGCGGACTTTAACCCGG-ATTTAGTAACTCGC
7015 ACAAATGCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
40 11 0.11
41 11 0.11
42 35 0.34
43 10 0.10
44 20 0.19
45 3 0.03
46 14 0.13
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (41 bp):
AATGCCTTCGCGGACTTTAACCCGGATTTAGTAACTCGCCC
Found at i:10835 original size:36 final size:39
Alignment explanation
Indices: 10681--10899 Score: 243
Period size: 40 Copynumber: 5.6 Consensus size: 39
10671 TTGAATGATG
* * * * *
10681 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
10721 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
10761 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
*
10800 TCCGGGTTAAGTCCCGAAGGCA-T-T-CGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
*
10836 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTA-AA
*
10877 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
10900 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
36 34 0.22
37 1 0.01
38 2 0.01
39 38 0.24
40 72 0.46
41 9 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:10864 original size:76 final size:77
Alignment explanation
Indices: 10681--10899 Score: 259
Period size: 76 Copynumber: 2.8 Consensus size: 77
10671 TTGAATGATG
* * * * *
10681 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCA-
*
10744 TTGTGCGAGATACTAAT
63 -T-TGCGAGATACTAAA
*
10761 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTG
*
10824 CGAGTTACTAAA
66 CGAGATACTAAA
* *
10836 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
10900 TGAACGAGGA
Statistics
Matches: 124, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
75 20 0.16
76 48 0.39
77 3 0.02
78 1 0.01
79 34 0.27
80 18 0.15
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (77 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTG
CGAGATACTAAA
Found at i:18648 original size:40 final size:40
Alignment explanation
Indices: 18564--18788 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
18554 TTGAATGATG
* * * *
18564 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
18604 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18644 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18683 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18723 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
18764 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18789 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:18810 original size:119 final size:119
Alignment explanation
Indices: 18564--18821 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
18554 TTGAATGATG
* *
18564 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
18629 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
18683 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
18746 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
18803 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
18822 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Done.