Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2539
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: 36128
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:2901 original size:17 final size:17
Alignment explanation
Indices: 2871--2917 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2861 TTAGCATTTA
2871 TTTATTTTCAATTTAAATT
1 TTTATTTT--ATTTAAATT
**
2890 TTTATTTTATTTTCATT
1 TTTATTTTATTTAAATT
2907 TTTATTTTATT
1 TTTATTTTATT
2918 CGTTCCTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 18 0.69
19 8 0.31
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTATTTAAATT
Found at i:15645 original size:36 final size:37
Alignment explanation
Indices: 15581--15685 Score: 160
Period size: 36 Copynumber: 2.9 Consensus size: 37
15571 AGCTGAGACG
* * *
15581 AAATCTCCATACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
15618 AAATCTCCACACGTAGTCA-CGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
15654 TAATCTCCACACGTAGTCATC-GGTCTTACCCG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCG
15686 AAATATATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
36 46 0.73
37 17 0.27
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:15956 original size:48 final size:48
Alignment explanation
Indices: 15835--16014 Score: 272
Period size: 48 Copynumber: 3.7 Consensus size: 48
15825 ACATCGCTAC
* * *
15835 ATTTCTCACTAGCCATTCGGCTTTACCACATATAACATATCTCATATATT
1 ATTTCACATTAGCCATTCGGCTTTACCACATAT-ACATATCTCATACA-T
* *
15885 ATTTCACATT-GACCATTCAGCTTTACCACATATGCATATCTCATACAT
1 ATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCATACAT
*
15933 ATTTCACATTAGCCATTCGGCTTTACCACATATACATTTCTCATACAT
1 ATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACAT
15981 ATTTCACATTAGCCATTCGGCTTTACCACATATA
1 ATTTCACATTAGCCATTCGGCTTTACCACATATA
16015 TGCATGTTCA
Statistics
Matches: 120, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
48 78 0.65
49 14 0.12
50 28 0.23
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (48 bp):
ATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACAT
Found at i:16117 original size:45 final size:46
Alignment explanation
Indices: 15984--16172 Score: 231
Period size: 45 Copynumber: 4.1 Consensus size: 46
15974 CATACATATT
* * * *
15984 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGC-CTATCACATATATGCATGTTCACATTCA
* * *
16031 CCACATTGGCCATTC-GCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCC-TATCACATATATGCATGTTCACATTCA
16077 TCACATTGGCCATTC-GCCTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTATCACATATATGCATGTTCACATTCA
* * * **
16122 TCAAATT-GCCATTCGGCCTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTATCACATATATGCATGTTCACATTCA
16167 TCACAT
1 TCACAT
16173 AAAATCCTAA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
44 7 0.06
45 62 0.50
46 42 0.34
47 13 0.10
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (46 bp):
TCACATTGGCCATTCGGCCTATCACATATATGCATGTTCACATTCA
Found at i:23919 original size:47 final size:48
Alignment explanation
Indices: 23865--23995 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 48
23855 CACAATCGAT
*
23865 AAGTACCTATACCATGACTCGTAGCCAAATCAAGGTAACTTATC-CCG
1 AAGTACCTATACCATGACTCGTAGCCAAATCAAGGTAACTCATCTCCG
* * * **
23912 GAGTACCTATACTATGA-TCGTAGCCAAATCAAGGTAACTCCTCTTTG
1 AAGTACCTATACCATGACTCGTAGCCAAATCAAGGTAACTCATCTCCG
* * * *
23959 AAATACCTATACCATGGCCCATAGCCAAATCAAGGTA
1 AAGTACCTATACCATGACTCGTAGCCAAATCAAGGTA
23996 TCATTTTCAC
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 24 0.34
47 29 0.41
48 17 0.24
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (48 bp):
AAGTACCTATACCATGACTCGTAGCCAAATCAAGGTAACTCATCTCCG
Found at i:26236 original size:47 final size:46
Alignment explanation
Indices: 26074--26425 Score: 156
Period size: 47 Copynumber: 7.5 Consensus size: 46
26064 TTTGTGCGCT
* * * * *
26074 AGTGTAAGACATGTCTGGGACATGC-TTCGGCCACATTACT-AGAGTC
1 AGTGTAAGACATGTCTGGGACATGCATT-AGCCATACTA-TGATAGCC
* * * * *
26120 AGTGTAAGACCATGTCTGAGACATGATATTAG-CAT-CCA-GACAAGGGCT
1 AGTGTAAGA-CATGTCTGGGACATG-CATTAGCCATACTATGA-TA--GCC
* *
26168 AGTGTAAGACATGTATTGGACATGCATTAGCCATACTATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCATACTATGATAGCC
** **
26214 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACA-AAGATGAGT-GCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATTAGC-CATACTATGA-TAGCC
** *
26262 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGAC-AGAGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCAT--ACTA-TGATAGCC
* * * ** *
26309 AGTGTAAGACGTGTCTGGGACACGCA-TCGCC-TAAGAGTTG-T-GCT
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCATACTA--TGATAGCC
* * *
26353 AGTGTAAGACATGTCTGGGACATGCATCAGCACGGGTA-TATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATTAGC-C--ATACTATGATAGCC
* *
26401 AGTGTAAGTCCATGTTTGGGACATG
1 AGTGTAAG-ACATGTCTGGGACATG
26426 ACATCAGCAA
Statistics
Matches: 236, Mismatches: 41, Indels: 55
0.71 0.12 0.17
Matches are distributed among these distances:
44 27 0.11
45 6 0.03
46 45 0.19
47 87 0.37
48 48 0.20
49 23 0.10
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATTAGCCATACTATGATAGCC
Found at i:26370 original size:44 final size:45
Alignment explanation
Indices: 26211--26380 Score: 193
Period size: 47 Copynumber: 3.7 Consensus size: 45
26201 TACTATGATA
* *
26211 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAAAGA-TGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTAAGAGT-TGT
* *
26259 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGAT-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT--A-AGAGTTGT
* *
26306 GCCAGTGTAAGACGTGTCTGGGACACGCATC-GCCTAAGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAAGAGTTGT
*
26350 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
26381 AGCACGGGTA
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
43 5 0.05
44 29 0.27
45 1 0.01
46 12 0.11
47 44 0.42
48 15 0.14
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAAGAGTTGT
Found at i:26373 original size:91 final size:94
Alignment explanation
Indices: 26071--26424 Score: 278
Period size: 94 Copynumber: 3.8 Consensus size: 94
26061 TGATTTGTGC
* * * * ** * *
26071 GCTAGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTACTAGAGTCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTAAGATAGCCAGTGTAAGACCATGTC
* * ** * ** *
26136 TGAGACAT-GATATTAGCATC-CAGACAAGG
66 TGGGACATCG-CATCGGCA-CAAAGATGAGT
* * * *
26165 GCTAGTGTAAGACATGTATTGGACATGCATTAGCCATACTATGATAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTAAGATAGCCAGTGTAAGACCATGTC
*
26230 TGGGACATGGCATCGGCACAAAGATGAGT
66 TGGGACATCGCATCGGCACAAAGATGAGT
* * *
26259 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGAC-AGAGATAGCCAGTGTAAGA-CGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ACTA-AGATAGCCAGTGTAAGACCAT
* *
26321 GTCTGGGACA-CGCATC-GC-CTAAGA-GTTGT
63 GTCTGGGACATCGCATCGGCACAAAGATG-AGT
* * * *
26350 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGGGTA-TATGAGAGCCAGTGTAAGTCCAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGC-C--ATACTAAGATAGCCAGTGTAAGACCAT
*
26414 GTTTGGGACAT
63 GTCTGGGACAT
26425 GACATCAGCA
Statistics
Matches: 211, Mismatches: 36, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
90 1 0.00
91 39 0.18
92 17 0.08
93 20 0.09
94 114 0.54
95 20 0.09
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTAAGATAGCCAGTGTAAGACCATGTC
TGGGACATCGCATCGGCACAAAGATGAGT
Done.