Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold434
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: 307070
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 3 of 3
Found at i:292228 original size:175 final size:175
Alignment explanation
Indices: 291923--292337 Score: 456
Period size: 175 Copynumber: 2.4 Consensus size: 175
291913 ACTCTAGATG
* * * *
291923 ACATTGACATTTGCATCATTTTATATGCATTTCCCACTTTATTGATGCTTACAGTTGCATCGTTT
1 ACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATGCTTGCA-TTGCATCATTT
* * ** * * * * *
291988 CATGCATATTTGCATTTTAGATAATGTTGGCATTTGCATCATTTCATGTGTATTTGCATCTTTAT
65 CACGCATATTTGCACTTTAGATAACCTTGGCAATGGCATCATATCATATGCATTTGCATCTTTAT
* * * * * *
292053 TGATGCTTGCAGTTGCATTTTTTCATGAACTTCTGCACGTTACATA
130 TGAAGCTAGCAGTTGCATTATTTCACGAACATCTACACGTTACATA
* * * *
292099 ACATTGGCATTTGCATTATTTCATATGCATTTTCCA-TTTATTAATGCTTGTATTTGCATCATTT
1 ACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATGCTTGCA-TTGCATCATTT
* * *
292163 CACGCATATTTGTACTTTAGATGACCTTGGTAATGGCATCATATCATATGCATTTGCCA-CTTTA
65 CACGCATATTTGCACTTTAGATAACCTTGGCAATGGCATCATATCATATGCATTTG-CATCTTTA
* * * * * *
292227 TTGAAGCTAGCATTTGTATTATTTCACGCACATCTACACTTTAGATG
129 TTGAAGCTAGCAGTTGCATTATTTCACGAACATCTACACGTTACATA
* * * * *
292274 ACATTGGTATTAGCATCATTTCATATACATTTGCCACTTTATTGATGCTTGCATTACATCATTT
1 ACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATGCTTGCATTGCATCATTT
292338 TACATACATA
Statistics
Matches: 196, Mismatches: 41, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
175 148 0.76
176 48 0.24
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (175 bp):
ACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATGCTTGCATTGCATCATTTC
ACGCATATTTGCACTTTAGATAACCTTGGCAATGGCATCATATCATATGCATTTGCATCTTTATT
GAAGCTAGCAGTTGCATTATTTCACGAACATCTACACGTTACATA
Found at i:292313 original size:45 final size:43
Alignment explanation
Indices: 292263--292371 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 43
292253 CGCACATCTA
* *
292263 CACTTTAGATGACATTGGTATTAGCATCATTTCATATACATTTG
1 CACTTTAGATGACATTGGTATTA-CATCATTTCACATACATATG
* *
292307 CCACTTTATTGATG-C-TT-GCATTACATCATTTTACATACATATG
1 -CACTTTA--GATGACATTGGTATTACATCATTTCACATACATATG
*
292350 CACTTTAGAGGACATTGGTATT
1 CACTTTAGATGACATTGGTATT
292372 TGCCTTGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
40 3 0.06
41 1 0.02
42 9 0.17
43 21 0.40
44 5 0.09
45 9 0.17
46 1 0.02
47 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (43 bp):
CACTTTAGATGACATTGGTATTACATCATTTCACATACATATG
Found at i:292357 original size:175 final size:176
Alignment explanation
Indices: 291904--292369 Score: 447
Period size: 175 Copynumber: 2.7 Consensus size: 176
291894 CGTTTTATGT
* * *
291904 ACATCTACAACTCTAGATGACATTGACATTTGCATCATTTTATATGCATTTCCCACTTTATTGAT
1 ACATCTAC-ACTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGAT
* * * * * ** * * * *
291969 GCTTACAGTTGCATC-GTTT-CATGCATATTTGCATTTTAGATAATGTTGGCATTTGCATCATTT
65 GCTTGCAGTTGCATCATTTTACATACATA--TGCACTTTAGATGACATTGGTAATGGCATCATAT
* * * * * *
292032 CATGTGTATTTGCATCTTTATTGATGCTTGCAGTTGCATTTTTTCATGA
128 CATATGCATTTGCATCTTTATTGAAGCTAGCAGTTGCATTATTTCACGA
* * * * * * * *
292081 ACTTCTGCACGTTACATAACATTGGCATTTGCATTATTTCATATGCATTTTCCA-TTTATTAATG
1 ACATCTACACTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATG
* * * ** * * * *
292145 CTTGTATTTGCATCATTTCACGCATATTTGTACTTTAGATGACCTTGGTAATGGCATCATATCAT
66 CTTGCAGTTGCATCATTTTACATACATATGCACTTTAGATGACATTGGTAATGGCATCATATCAT
* * *
292210 ATGCATTTGCCA-CTTTATTGAAGCTAGCATTTGTATTATTTCACGC
131 ATGCATTTG-CATCTTTATTGAAGCTAGCAGTTGCATTATTTCACGA
* * * *
292256 ACATCTACACTTTAGATGACATTGGTATTAGCATCATTTCATATACATTTGCCACTTTATTGATG
1 ACATCTACACTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATG
* *
292321 CTTGCA-TTACATCATTTTACATACATATGCACTTTAGAGGACATTGGTA
66 CTTGCAGTTGCATCATTTTACATACATATGCACTTTAGATGACATTGGTA
292370 TTTGCCTTGT
Statistics
Matches: 225, Mismatches: 60, Indels: 10
0.76 0.20 0.03
Matches are distributed among these distances:
175 160 0.71
176 56 0.25
177 9 0.04
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (176 bp):
ACATCTACACTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTCCCACTTTATTGATG
CTTGCAGTTGCATCATTTTACATACATATGCACTTTAGATGACATTGGTAATGGCATCATATCAT
ATGCATTTGCATCTTTATTGAAGCTAGCAGTTGCATTATTTCACGA
Found at i:292985 original size:60 final size:59
Alignment explanation
Indices: 292866--293093 Score: 185
Period size: 60 Copynumber: 3.8 Consensus size: 59
292856 TTCTATTTAG
* * *
292866 GCCATTTCATTGAATCTTGGTTTTGCAAAAGTCATTGTTTAGGTTTCTCGTTTCGTTCAA
1 GCCATTTCATTGAATCTTGGTTTTGC-CAAGTCATTGTTTAGGTTTCTCATTTCATTCAA
** * * * * *
292926 GTTATTT-AGTTGAGTCTTGGTTTTGGCCAACTCATTGTTTAGGTTTTTTATTTTATTCAA
1 GCCATTTCA-TTGAATCTTGGTTTT-GCCAAGTCATTGTTTAGGTTTCTCATTTCATTCAA
* * * * ** * *
292986 GCCATTTCATTGACTCTTTGTTTTTCCCAAGTTATTGTTTAGGTTGT-TGGTTTGATCCAA
1 GCCATTTCATTGAATC-TTGGTTTTGCCAAGTCATTGTTTAGGTT-TCTCATTTCATTCAA
*
293046 GCCATTTCATT-AAGTCTTAGTTTTGCCCAAGTCATT-TTGTAGGTTTCT
1 GCCATTTCATTGAA-TCTTGGTTTTG-CCAAGTCATTGTT-TAGGTTTCT
293094 AATGTCATCA
Statistics
Matches: 133, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
59 11 0.08
60 111 0.83
61 11 0.08
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (59 bp):
GCCATTTCATTGAATCTTGGTTTTGCCAAGTCATTGTTTAGGTTTCTCATTTCATTCAA
Found at i:293558 original size:13 final size:13
Alignment explanation
Indices: 293540--293564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
293530 CATAAAGTGT
293540 TGTATCGATACAA
1 TGTATCGATACAA
293553 TGTATCGATACA
1 TGTATCGATACA
293565 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:293576 original size:33 final size:33
Alignment explanation
Indices: 293520--293586 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
293510 TTCAACGATT
*
293520 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
*** *
293553 TGTATCGATACATATTTTTTTGTATCAATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
293586 T
1 T
293587 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCAATACAA
Found at i:293645 original size:13 final size:13
Alignment explanation
Indices: 293627--293651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
293617 ATCACTTAAA
293627 TGTATCGATACAT
1 TGTATCGATACAT
293640 TGTATCGATACA
1 TGTATCGATACA
293652 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.