Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2609
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: 50820
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7146 original size:24 final size:24
Alignment explanation
Indices: 7096--7149 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
7086 AATCGAATTT
*
7096 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
7120 GCACACATAGTGCCATAG-CACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
7144 GCACAC
1 GCACAC
7150 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 6 0.22
26 2 0.07
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.15
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:14756 original size:29 final size:29
Alignment explanation
Indices: 14723--14782 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
14713 GCGAGACCAG
14723 ATGTTAGAACACCTGCAAGGACCTATGCT
1 ATGTTAGAACACCTGCAAGGACCTATGCT
* *
14752 ATGTTAGAGCACCTGCAAGGACTTATGCT
1 ATGTTAGAACACCTGCAAGGACCTATGCT
14781 AT
1 AT
14783 TCGTGCTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (29 bp):
ATGTTAGAACACCTGCAAGGACCTATGCT
Found at i:19581 original size:53 final size:53
Alignment explanation
Indices: 19398--19604 Score: 207
Period size: 53 Copynumber: 3.8 Consensus size: 53
19388 ATTAGGGTTT
* * * * *
19398 AAGGATACCAAGTAAGACCATGCCAAGACATGACATTGGTAAGTTTTACAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGAC
* * * * * * * *
19452 AAGGAAATCATGTAAGACCATGTCAAAACATGGCATTGATAAACTACGATAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGAC
* * * * *
19507 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGAC
* *
19560 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
19605 TAAAAAGGAA
Statistics
Matches: 121, Mismatches: 30, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
53 45 0.37
54 37 0.31
55 39 0.32
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGAC
Found at i:24018 original size:46 final size:46
Alignment explanation
Indices: 23951--24079 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
23941 TGTAACCCGC
* * * *
23951 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
23997 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
24043 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
24080 TGCCCAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:25389 original size:13 final size:13
Alignment explanation
Indices: 25371--25400 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25361 GGATATTACA
25371 AGATTGATGTTAT
1 AGATTGATGTTAT
*
25384 AGATTGATGTTTT
1 AGATTGATGTTAT
25397 AGAT
1 AGAT
25401 GGTTTAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (13 bp):
AGATTGATGTTAT
Found at i:30453 original size:78 final size:78
Alignment explanation
Indices: 30317--30529 Score: 274
Period size: 78 Copynumber: 2.7 Consensus size: 78
30307 AAGCCAAGTA
* * * * *
30317 CCTTCGGGATTTA-ACCGGATATAGCTACTCACTC-AATGCCTTCGGGACATAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAG-CCGGATATAG
*
30380 TAACTCGCACCAATG
64 TAACTCGCACAAATG
30395 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGACTTAGCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
30459 AACTCGCACAAATG
65 AACTCGCACAAATG
30473 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATGCCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACT--CGCACAAATGCCTTCGGGACTTAGCC
30530 CGTTATCATC
Statistics
Matches: 121, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
77 1 0.01
78 64 0.53
79 33 0.27
80 23 0.19
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCGGATATAGTA
ACTCGCACAAATG
Found at i:30461 original size:38 final size:40
Alignment explanation
Indices: 30317--30531 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
30307 AAGCCAAGTA
* * * *
30317 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCACTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
30355 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30395 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30435 CCTTC-GGACTTAG-CCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
30473 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
30514 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
30532 TTATCATCCA
Statistics
Matches: 161, Mismatches: 8, Indels: 13
0.88 0.04 0.07
Matches are distributed among these distances:
38 42 0.26
39 33 0.20
40 59 0.37
41 23 0.14
42 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38625 original size:39 final size:40
Alignment explanation
Indices: 38428--38645 Score: 291
Period size: 40 Copynumber: 5.5 Consensus size: 40
38418 AAGCCAAGTA
* * * *
38428 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
38467 CCTTCGGGACATAGCCCGGATATATATAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATA-GTAACTCGCACAAATG
38508 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38548 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38588 CCTTC-GGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
38627 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
38646 TTATCATCCA
Statistics
Matches: 162, Mismatches: 12, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 45 0.28
40 82 0.51
41 34 0.21
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38628 original size:79 final size:81
Alignment explanation
Indices: 38428--38645 Score: 284
Period size: 79 Copynumber: 2.7 Consensus size: 81
38418 AAGCCAAGTA
* * * * * *
38428 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
38491 TATAACTCGCACCAATG
65 TATAACTCGCACAAATG
*
38508 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA-
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAT
*
38572 GTAACTCGCACAAATG
66 ATAACTCGCACAAATG
* *
38588 CCTTC-GGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
38646 TTATCATCCA
Statistics
Matches: 125, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
78 1 0.01
79 48 0.38
80 32 0.26
81 44 0.35
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (81 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAT
ATAACTCGCACAAATG
Found at i:44145 original size:82 final size:79
Alignment explanation
Indices: 44006--44224 Score: 232
Period size: 82 Copynumber: 2.7 Consensus size: 79
43996 TTGATGATAA
* * *
44006 CCGGGCTAAAGT-CCGAAGGCATTTGCGCT-AGTGACTAGT-TCCGGGCTAAGTCTCGAAGGCAT
1 CCGGGCT-AAGTCCCGAAGGCATTTGAG-TGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCAT
*
44068 TTGTGCGAGTTACTATAATT
63 TGGTGCGA-TTACTAT-A-T
*
44088 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
*
44153 TGCGATTATTATAT
66 TGCGATTACTATAT
* * * * * *
44167 CTGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
44225 TACTTGGCTT
Statistics
Matches: 121, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
78 16 0.13
79 35 0.29
80 1 0.01
81 12 0.10
82 57 0.47
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
TGCGATTACTATAT
Found at i:44180 original size:39 final size:40
Alignment explanation
Indices: 44006--44224 Score: 241
Period size: 40 Copynumber: 5.5 Consensus size: 40
43996 TTGATGATAA
* * *
44006 CCGGGCTAAAGT-CCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
44046 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-A-T
*
44088 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
44128 CCGGGCTAAGTCCCGAAGGCATTGGTGCGA-TTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
44167 CTGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
44207 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
44225 TACTTGGCTT
Statistics
Matches: 155, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
39 54 0.35
40 63 0.41
41 1 0.01
42 37 0.24
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.