Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1712
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: 15646
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:5369 original size:40 final size:41
Alignment explanation
Indices: 5227--5412 Score: 234
Period size: 41 Copynumber: 4.6 Consensus size: 41
5217 TACTCGAATG
* *
5227 ATATCCGGGCTAAGTCCTGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
5268 ATATCCGGGCTATGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* * *
5309 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCT-AGCAACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGCGACT
* * *
5349 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCT-AGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
5389 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
5413 CTTGTGCGAG
Statistics
Matches: 128, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 60 0.47
41 66 0.52
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (41 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
Found at i:5372 original size:81 final size:82
Alignment explanation
Indices: 5229--5382 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 82
5219 CTCGAATGAT
* * * * *
5229 ATCCGGGCTAAGTCCTGAAGGCTTTTGTGCTAAGCGACTATATCCGGGCTATGTCCCGAAGGCTT
1 ATCCGGACTAAGTCCTGAAGGCATTTGTGCTAAGCAACTATATCCGGGCTAAGTCCCGAAGGCAT
*
5294 TTGTGCTAAGCGACTAC
66 TTATGCTAAGCGACTAC
5311 ATCCGGACTAAGATCC-GAAGGCATTTGTGCT-AGCAACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATCCGGACTAAG-TCCTGAAGGCATTTGTGCTAAGCAACTATATCCGGGCTAAGTCCCGAAGGCA
5374 TTTATGCTA
65 TTTATGCTA
5383 GTGACCATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 37 0.57
82 25 0.38
83 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (82 bp):
ATCCGGACTAAGTCCTGAAGGCATTTGTGCTAAGCAACTATATCCGGGCTAAGTCCCGAAGGCAT
TTATGCTAAGCGACTAC
Found at i:7827 original size:27 final size:27
Alignment explanation
Indices: 7796--8064 Score: 319
Period size: 27 Copynumber: 10.0 Consensus size: 27
7786 ACCTAATTGA
* * *
7796 TAAAATGATTGTTTTGTCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
** * *
7823 TAAAATGGTTGTTTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
7850 TAAAATGGCTACTTTT-CCCTTATGTGG
1 TAAAATGACTA-TTTTGCCCTTATGTGG
7877 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
7904 TAAAATGATTATTTTTCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
7931 TAAAATGACTGTTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
7958 TAAAATGACTATTTTGTCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* * *
7985 TAGAATGA--ATGTTTGCCCTATATATGA
1 TAAAATGACTAT-TTTGCCCT-TATGTGG
*
8012 TAAAATGACTATTTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
8039 TAAGATGACTATTTTGCCCCTATGTG
1 TAAAATGACTATTTTGCCCTTATGTG
8065 AGGTATATAT
Statistics
Matches: 213, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
25 2 0.01
26 11 0.05
27 186 0.87
28 12 0.06
29 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGG
Found at i:8412 original size:18 final size:18
Alignment explanation
Indices: 8389--8423 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8379 CTGTTTAAAC
8389 TGTTACTACACTGTTTAT
1 TGTTACTACACTGTTTAT
*
8407 TGTTACTGCACTGTTTA
1 TGTTACTACACTGTTTA
8424 CTATTATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (18 bp):
TGTTACTACACTGTTTAT
Found at i:10455 original size:28 final size:28
Alignment explanation
Indices: 10392--10489 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
10382 ATATTAAGTA
*
10392 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
10419 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
10447 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
10476 CGCACACTTAGTGC
1 CGCACACTTAGTGC
10490 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:15198 original size:41 final size:41
Alignment explanation
Indices: 15141--15222 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
15131 TATTACATTA
*
15141 ACATGTATTAGCCATGATTGTGGATGTTTTGGTTGCCTAAG
1 ACATGTATTAGCCATGATTGTAGATGTTTTGGTTGCCTAAG
15182 ACATGTATTAGCCATGATTGTAGATGTTTTGGTTGCCTAAG
1 ACATGTATTAGCCATGATTGTAGATGTTTTGGTTGCCTAAG
15223 TATACTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (41 bp):
ACATGTATTAGCCATGATTGTAGATGTTTTGGTTGCCTAAG
Done.