Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3736
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: 17447
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:225 original size:1 final size:1
Alignment explanation
Indices: 219--256 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
209 ATTAAGTAAC
219 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
257 GAGGTTTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5326 original size:45 final size:45
Alignment explanation
Indices: 5120--5322 Score: 299
Period size: 45 Copynumber: 4.6 Consensus size: 45
5110 CTGAATTCAT
* *
5120 TCACCGGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-ATA
* *
5162 TCA-CAGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATA
5206 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATA
* *
5251 TCACCGGTATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATA
*
5296 TCACCGGCACTATAGCCTGCTAGGCTC
1 TCACCGGCATTATAGCCTGCTAGGCTC
5323 AAAGACCCAA
Statistics
Matches: 146, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
41 6 0.04
42 20 0.14
43 5 0.03
44 8 0.05
45 107 0.73
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATA
Found at i:6695 original size:37 final size:37
Alignment explanation
Indices: 6645--6724 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
6635 CTTATTACGA
* *
6645 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
6682 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
6719 GGTCTT
1 AGTCTT
6725 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:6914 original size:47 final size:47
Alignment explanation
Indices: 6843--7247 Score: 562
Period size: 47 Copynumber: 8.6 Consensus size: 47
6833 CCCTTCGGGA
** * *
6843 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
6890 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
6937 CTTATCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
6984 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
7031 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
7078 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
7125 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
7173 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
7220 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
7248 TATTCAATTA
Statistics
Matches: 327, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
46 1 0.00
47 264 0.81
48 61 0.19
49 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:9662 original size:47 final size:47
Alignment explanation
Indices: 9592--9740 Score: 253
Period size: 47 Copynumber: 3.2 Consensus size: 47
9582 GGCTTATCAT
* * *
9592 ATTTAACAAGGTTAACTACGTAACTTATCCGAAAATAGTAAGAACAA
1 ATTTAACAAGCTTAACTAAGTAACTTATCCGGAAATAGTAAGAACAA
*
9639 ATTTAACAAGCTTAACTAAGTAACTTATCCGGAAATATTAAGAACAA
1 ATTTAACAAGCTTAACTAAGTAACTTATCCGGAAATAGTAAGAACAA
*
9686 ATTTAACAAGCTTAACTAAGGAACTTATCCGGAAATAGTAAGAACAA
1 ATTTAACAAGCTTAACTAAGTAACTTATCCGGAAATAGTAAGAACAA
9733 ATTTAACA
1 ATTTAACA
9741 TCACTTCATC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (47 bp):
ATTTAACAAGCTTAACTAAGTAACTTATCCGGAAATAGTAAGAACAA
Found at i:13602 original size:34 final size:35
Alignment explanation
Indices: 13544--13615 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
13534 CGTATCCTAG
*
13544 CTACAGTCTCAGTCTTCTAAAGTTTTCAGT-TTTCC
1 CTACAGTCTCAGTCTTCTAAAG-TTTCAGTATTACC
* *
13579 CTACTGTCTCAGT-TTCTACAGTTTCAGTATTACC
1 CTACAGTCTCAGTCTTCTAAAGTTTCAGTATTACC
13613 CTA
1 CTA
13616 ACTACAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 14 0.42
35 12 0.36
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (35 bp):
CTACAGTCTCAGTCTTCTAAAGTTTCAGTATTACC
Found at i:17212 original size:34 final size:37
Alignment explanation
Indices: 17146--17217 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 37
17136 CTAGCTACAG
* *
17146 TCTCAGTCTTCTAAAGTTTTCAGTTTTCCCCT-ACTA
1 TCTCAGTCTTCTAAAGTTTTCAGTATTACCCTAACTA
*
17182 TCTCAGT-TTCTACAG-TTTCAGTATTACCCTAACTA
1 TCTCAGTCTTCTAAAGTTTTCAGTATTACCCTAACTA
17217 T
1 T
17218 AGAATTAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 13 0.41
35 12 0.38
36 7 0.22
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.43
Consensus pattern (37 bp):
TCTCAGTCTTCTAAAGTTTTCAGTATTACCCTAACTA
Done.