Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold688
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: 346233
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:60353 original size:24 final size:24
Alignment explanation
Indices: 60326--60398 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
60316 CTTTCCTTTT
60326 TGTCTTGACTCTATGCCTTCCAGC
1 TGTCTTGACTCTATGCCTTCCAGC
* **
60350 TGTCTTGGCT-T-T-CCTT---TT
1 TGTCTTGACTCTATGCCTTCCAGC
60368 TGTCTTGACTCTATGCCTTCCAGC
1 TGTCTTGACTCTATGCCTTCCAGC
60392 TGTCTTG
1 TGTCTTG
60399 GTGAAGACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 9 0.24
19 1 0.03
20 1 0.03
21 8 0.22
22 1 0.03
23 1 0.03
24 16 0.43
ACGTcount: A:0.08, C:0.29, G:0.18, T:0.45
Consensus pattern (24 bp):
TGTCTTGACTCTATGCCTTCCAGC
Found at i:60370 original size:42 final size:42
Alignment explanation
Indices: 60311--60399 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
60301 TCATTCCTGG
60311 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
1 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
60353 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
1 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
60395 CTTGG
1 CTTGG
60400 TGAAGACTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.07, C:0.28, G:0.18, T:0.47
Consensus pattern (42 bp):
CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
Found at i:98990 original size:17 final size:17
Alignment explanation
Indices: 98968--99003 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
98958 GGGAAGATAG
98968 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
98985 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
99002 AG
1 AG
99004 CTAAGGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.31, T:0.03
Consensus pattern (17 bp):
AGAAAGAGAGACAAGAA
Found at i:112111 original size:78 final size:78
Alignment explanation
Indices: 111981--112134 Score: 263
Period size: 78 Copynumber: 2.0 Consensus size: 78
111971 AAACTCAAAT
* * *
111981 TGTAACCTCCCGGTCTGCCGTCTCCACGACTTTCCCTTTGGCGGGCTGCTCCTCAAGCCTTCGAG
1 TGTAACCTCCCGGTCTACCGTCTCCACGACTTTCCCTTTGGCGGGCTACTCCTCAAGCCTTCAAG
*
112046 TGCCGATCTTCGC
66 TGCCAATCTTCGC
*
112059 TGTAACCTCCCGGTCTACCGTCTCCACGACTTTCCCTTTGGTGGGCTACTCCTCAAGCCTTCAAG
1 TGTAACCTCCCGGTCTACCGTCTCCACGACTTTCCCTTTGGCGGGCTACTCCTCAAGCCTTCAAG
112124 TGCCAATCTTC
66 TGCCAATCTTC
112135 ACTTGGGCCG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.13, C:0.38, G:0.20, T:0.29
Consensus pattern (78 bp):
TGTAACCTCCCGGTCTACCGTCTCCACGACTTTCCCTTTGGCGGGCTACTCCTCAAGCCTTCAAG
TGCCAATCTTCGC
Found at i:229291 original size:17 final size:17
Alignment explanation
Indices: 229271--229306 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
229261 ATATCCTTAG
229271 CTTTCCTGTATCTCTTT
1 CTTTCCTGTATCTCTTT
* *
229288 CTTTCTTGTCTCTCTTT
1 CTTTCCTGTATCTCTTT
229305 CT
1 CT
229307 CTATCTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTTCCTGTATCTCTTT
Found at i:271473 original size:16 final size:17
Alignment explanation
Indices: 271441--271486 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
271431 CATCCCTTGG
271441 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
271458 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
271474 GCTTAGTTTATTC
1 GGTTAGTTCATTC
271487 CATTTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Found at i:298545 original size:26 final size:26
Alignment explanation
Indices: 298509--298561 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
298499 GGGACAAAGG
298509 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
298535 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
298561 C
1 C
298562 ATAGCGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.23, T:0.30
Consensus pattern (26 bp):
CCTCGAATCCTGTCTTTGACGGCGAT
Found at i:307096 original size:14 final size:14
Alignment explanation
Indices: 307077--307107 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
307067 TTTGAATTAT
307077 AATGCCACTAATCC
1 AATGCCACTAATCC
*
307091 AATGCCGCTAATCC
1 AATGCCACTAATCC
307105 AAT
1 AAT
307108 AGTTTAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGCCACTAATCC
Found at i:316356 original size:2 final size:2
Alignment explanation
Indices: 316349--316385 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
316339 ACCTTTTTAG
*
316349 TA TA TA TA TA AA TA TA TA TA TA TA TA TA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
316386 CTTTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Done.