Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7592.1
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: 6568
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Found at i:4015 original size:10 final size:9
Alignment explanation
Indices: 4000--4061 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
3990 TCTATTTCAA
4000 AAAAAAAATG
1 AAAAAAAA-G
4010 AAAAAAAAG
1 AAAAAAAAG
4019 AAAAGAAAAGG
1 AAAA-AAAA-G
4030 AAAAAATAA-
1 AAAAAA-AAG
*
4039 AATAAAAAG
1 AAAAAAAAG
4048 --AAAAAAG
1 AAAAAAAAG
4055 AAAAAAA
1 AAAAAAA
4062 TGGAGAGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
7 6 0.14
8 2 0.05
9 15 0.34
10 14 0.32
11 7 0.16
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:4033 original size:19 final size:18
Alignment explanation
Indices: 4012--4058 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
4002 AAAAAATGAA
*
4012 AAAAAAGAAAAGAAAAGG
1 AAAAAAGAAAAGAAAAAG
* *
4030 AAAAAATAAAATAAAAAG
1 AAAAAAGAAAAGAAAAAG
4048 AAAAAAGAAAA
1 AAAAAAGAAAA
4059 AAATGGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (18 bp):
AAAAAAGAAAAGAAAAAG
Found at i:5070 original size:43 final size:43
Alignment explanation
Indices: 5018--5159 Score: 116
Period size: 43 Copynumber: 3.3 Consensus size: 43
5008 AGTGCCTTAA
5018 TCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATC
1 TCCC-TAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATC
* * * * * *
5062 TCCCTAAGCAGTAGTGG-AGCTGATCGAAGA-CT-C-GCT-TTAATC
1 TCCCTAAGCAGTAG-GGTAACAGGT-TAA-ATTTGCAGATCTT-ATC
**
5104 -CCCTAAGTGGTAGGGTAACAGGTTAAATTTGCAGATCTTATC
1 TCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATC
*
5146 TCTCTAAGCAGTAG
1 TCCCTAAGCAGTAG
5160 TGGAGCAGAT
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 18 0.25
42 10 0.14
43 27 0.38
44 9 0.13
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (43 bp):
TCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATC
Found at i:5155 original size:84 final size:84
Alignment explanation
Indices: 5011--5459 Score: 587
Period size: 84 Copynumber: 5.4 Consensus size: 84
5001 AAAATTCAGT
*
5011 GCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
5076 TGGAGCTGATCGAAGACTC
66 TGGAGCAGATCGAAGACTC
* ** *
5095 GCTTTAATCCCCTAAGTGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCTCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
5160 TGGAGCAGATCAAAGACTC
66 TGGAGCAGATCGAAGACTC
*
5179 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTT-CA----CAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
5239 TAGAGCAGATCGAAGACTC
66 TGGAGCAGATCGAAGACTC
* * * * * * *
5258 GCCTTAATCTCCTAAGTAGTAGAGTAACAGG-----GTCGCAAATCTTATCTCCCTAAGTAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
5318 CGGAGCAGATCGATGACGACTC
66 TGGAGCAGATCGA--A-GACTC
* * *
5340 GCCTTAATCCCCTAAGCAATTGGGTAACAGGTTAAATTTGCAGATCTTATCTCCTTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
5405 TGGAGTAGATCGAAGA-TGC
66 TGGAGCAGATCGAAGACT-C
*
5424 ACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
5460 GGATAGCAGA
Statistics
Matches: 316, Mismatches: 36, Indels: 26
0.84 0.10 0.07
Matches are distributed among these distances:
79 103 0.33
81 1 0.00
82 31 0.10
83 2 0.01
84 143 0.45
85 1 0.00
87 35 0.11
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (84 bp):
GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACTC
Found at i:5194 original size:41 final size:41
Alignment explanation
Indices: 5149--5279 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
5139 TCTTATCTCT
5149 CTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATCCC
1 CTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATCCC
* * *
5190 CTAAGCAGTAG-GGTAACAGGTTCACAGA-T---CTT-ATCTCC
1 CTAAGCAGTAGTGG-AGCA-GATCAAAGACTCGCCTTAATC-CC
* * *
5228 CTAAGCAGTAGTAGAGCAGATCGAAGACTCGCCTTAATCTC
1 CTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATCCC
*
5269 CTAAGTAGTAG
1 CTAAGCAGTAG
5280 AGTAACAGGG
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
37 9 0.13
38 20 0.28
39 1 0.01
40 2 0.03
41 29 0.41
42 10 0.14
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (41 bp):
CTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATCCC
Found at i:5748 original size:87 final size:89
Alignment explanation
Indices: 5578--5782 Score: 263
Period size: 87 Copynumber: 2.3 Consensus size: 89
5568 ATTCGACGGA
* *
5578 GAGCAGATCGAAGACATAGCAGATCTGACCTTCGAATATTTTCACATTAAAGCAGATCCAAGATG
1 GAGCAGATCGAAGACATAGCAGATCTGACCTTCGAATAGTTTCACACTAAAGCAGATCCAAGATG
* *
5643 ATTTAGCATCCTTTTGTTTACAAG
66 ATTTAGCATCCCTGTGTTTACAAG
* * * * *
5667 GAGCAAATCGAAGACATAACAGATCTGACCTTC-AGGT-GTTT-ACGCTGAAGCAGATCCAAGAT
1 GAGCAGATCGAAGACATAGCAGATCTGACCTTCGA-ATAGTTTCACACTAAAGCAGATCCAAGAT
* *
5729 GATTTGGCATCCCTGTGTTTACAGG
65 GATTTAGCATCCCTGTGTTTACAAG
* *
5754 GAACAGATTGAAGACATAGCAGATCTGAC
1 GAGCAGATCGAAGACATAGCAGATCTGAC
5783 ATTCCTGTGC
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
87 64 0.64
88 4 0.04
89 32 0.32
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (89 bp):
GAGCAGATCGAAGACATAGCAGATCTGACCTTCGAATAGTTTCACACTAAAGCAGATCCAAGATG
ATTTAGCATCCCTGTGTTTACAAG
Found at i:6386 original size:19 final size:19
Alignment explanation
Indices: 6362--6459 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
6352 AATCTTTAAG
6362 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6381 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6400 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6417 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6436 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
6457 GAT
1 GAT
6460 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:6392 original size:36 final size:35
Alignment explanation
Indices: 6352--6459 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
6342 ATGGAAATAT
6352 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
6388 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
6424 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
6460 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Done.