Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4291
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: 15248
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:2445 original size:41 final size:41
Alignment explanation
Indices: 2365--2574 Score: 128
Period size: 41 Copynumber: 5.3 Consensus size: 41
2355 AGGCCTCGGT
* *
2365 CTTAGCCCGGTATATGGTCACTTAGCACAGATGCCTTCGGGA
1 CTTAGCCCGG-ATATAGTCACTTAGCACAAATGCCTTCGGGA
* *
2407 CTTAGCCCGGATATAGTCGC-TAGCACAAAATGCCTTCGGGT
1 CTTAGCCCGGATATAGTCACTTAGCAC-AAATGCCTTCGGGA
* * * *
2448 CTTAGCCCGGA-ATA---A-ATCGCA-AACAT-ACTTC-GGT
1 CTTAGCCCGGATATAGTCACTTAGCACAA-ATGCCTTCGGGA
* *
2482 CTTAG-CCGCGATATAG-CAAAC-TCGCACGAATGCCCTTC-GGA
1 CTTAGCCCG-GATATAGTC--ACTTAGCACAAATG-CCTTCGGGA
* * *
2523 CTTAGTCCGGTTATAGTCACCTAGCAC-AA-GCC-TCGGGA
1 CTTAGCCCGGATATAGTCACTTAGCACAAATGCCTTCGGGA
2561 CTTAGCCCGGATAT
1 CTTAGCCCGGATAT
2575 CATTCGAATA
Statistics
Matches: 137, Mismatches: 14, Indels: 38
0.72 0.07 0.20
Matches are distributed among these distances:
33 3 0.02
34 10 0.07
35 9 0.07
36 2 0.01
37 6 0.04
38 17 0.12
39 9 0.07
40 14 0.10
41 53 0.39
42 14 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (41 bp):
CTTAGCCCGGATATAGTCACTTAGCACAAATGCCTTCGGGA
Found at i:9592 original size:47 final size:47
Alignment explanation
Indices: 9540--9753 Score: 311
Period size: 47 Copynumber: 4.5 Consensus size: 47
9530 GATAATTGTG
* *
9540 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
9587 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
9634 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGCGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
9681 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
9728 ATGTGAAAAGTGTATAAATGTGATAA
1 ATGTG-AAAGTGTATATATGTGATAA
9754 TCCCGAAGGG
Statistics
Matches: 150, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
47 133 0.89
48 17 0.11
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:11951 original size:38 final size:38
Alignment explanation
Indices: 11887--11961 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
11877 AATCCGAGTT
*
11887 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
11925 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
11962 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:12113 original size:40 final size:40
Alignment explanation
Indices: 12018--12330 Score: 452
Period size: 40 Copynumber: 7.8 Consensus size: 40
12008 CGACGATGAT
*
12018 CGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT-C
12059 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
12099 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
*
12139 C-GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT-TATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
12177 C-GGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * *
12216 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* ** * * * *
12256 CGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * *
12296 CGGGCTAGGTCCCCGAAGAGCAATCATGCTGGTGA
1 CGGGCTAAGT-CCCGAAGAGCATTCATGCTAGTGA
12331 CGTGTATTCG
Statistics
Matches: 250, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
38 37 0.15
39 37 0.15
40 117 0.47
41 59 0.24
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
Found at i:12231 original size:117 final size:119
Alignment explanation
Indices: 12012--12330 Score: 482
Period size: 117 Copynumber: 2.7 Consensus size: 119
12002 AAGTCTCGAC
* *
12012 GATG-ATCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT-CCGGGCTAAGTCCCGAAG
12076 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
65 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
12131 GATGTATCCGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT-TATCC-GGCTAAGTCCCGAAGA
1 GATGTATCCGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGA
* *
12194 GCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
66 GCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* ** * * *
12248 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCCGAA
1 GATGTATCCG-GCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGT-CCCGAA
* *
12313 GAGCAATCATGCTGGTGA
64 GAGCATTCATGCTAGTGA
12331 CGTGTATTCG
Statistics
Matches: 184, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
117 77 0.42
118 30 0.16
119 12 0.07
120 43 0.23
121 22 0.12
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (119 bp):
GATGTATCCGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGA
GCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Done.